def __init__(self, parent=None):
"""Initialize the class.
Parameters
----------
parent : None, optional
Top-level widget.
"""
super().__init__(parent)
self.setupUi(self)
p1 = self.scatterPlot.addPlot()
self.scatterPlotItem = ScatterPlotItem()
p1.addItem(self.scatterPlotItem)
p1.setLabel('left', 'Y', units='pixel')
p1.setLabel('bottom', 'X', units='pixel')
self.yHistogramItem = None
self.xHistogramItem = None
self.numBins = 40
self.dataSize = None
self.xData = None
self.yData = None
self.rollArray = False
self.dataCounter = 0
self.brushes = None
self.brushColor = (159, 159, 159)
self.penColor = (255, 255, 255)
self.maxAlpha = 255
self.minAlpha = 127
self.histogramFillBrush = mkBrush(*self.brushColor, 200)
self.pointBrush = mkBrush(*self.brushColor, self.maxAlpha)
self.pointPen = mkPen(*self.penColor)
self.scatterPlotItem.setBrush(self.pointBrush)
def __init__(self, *args, **kwargs):
self.centerplot = ScatterPlotItem(brush="r")
self.centerplot.setZValue(100)
super(CenterMarker, self).__init__(*args, **kwargs)
self.addItem(self.centerplot)
self.drawCenter()
def scatter(self,
x: np.ndarray,
y: np.ndarray,
label: Optional[str] = None,
symbol: Optional[list] = None,
**kwargs) -> None:
kwargs = Axes._add_label_to_kwargs(label, kwargs)
item = ScatterPlotItem(**kwargs)
item.setData(x=x, y=y)
self._raw.addItem(item)
def __init__(self, manager: BarManager, am: ArrayManager):
""""""
ScatterPlotItem.__init__(self)
# ExChartItem.__init__(self,manager)
# super(TradeItem,self).__init__(manager, am)
super(ExChartItem, self).__init__(manager, am)
self.blue_pen: QtGui.QPen = pg.mkPen(color=(100, 100, 255), width=2)
self.trades: Dict[int, Dict[str,
TradeData]] = {} # {ix:{tradeid:trade}}
class ScatterPlotterNode(Node):
nodeName = 'ScatterPlotter'
sigUpdatePlot = QtCore.Signal(object)
def __init__(self, name):
Node.__init__(self,
name,
terminals={
'x': {
'io': 'in'
},
'y': {
'io': 'in'
},
'color': {
'io': 'in'
},
'plotItem': {
'io': 'out'
}
})
self.ScatterPlotItem = ScatterPlotItem(pen=None,
symbol='o',
size=2,
brush=(255, 255, 255, 160))
self.sigUpdatePlot.connect(self.updatePlot)
def updatePlot(self, xyb):
x, y, brs = xyb
self.ScatterPlotItem.setData(x, y)
if not brs is None:
self.ScatterPlotItem.setBrush(brs)
def process(self, x, y, color, display=True):
if x is None or y is None:
raise Exception('set proper inputs')
brs = None
if not color is None:
brs = [
fn.mkBrush(tuple(c)) for c in (color * 255).astype(np.int32)
]
self.sigUpdatePlot.emit((x, y, brs))
return {'plotItem': self.ScatterPlotItem}
def plotCurveAndFit(self, xData, yData):
# noinspection PyTypeChecker
self.plotAttributes["curve"] = ScatterPlotItem(xData,
yData,
pen=1,
symbol='x',
size=5)
self.plot.addItem(self.plotAttributes["curve"])
self.plotFit(xData, yData,
self.devices["B"] + ' vs. ' + self.devices["A"])
class CenterMarker(QSpace):
def __init__(self, *args, **kwargs):
self.centerplot = ScatterPlotItem(brush="r")
self.centerplot.setZValue(100)
super(CenterMarker, self).__init__(*args, **kwargs)
self.addItem(self.centerplot)
self.drawCenter()
def drawCenter(self):
try:
fit2d = self._geometry.getFit2D()
except (TypeError, AttributeError):
pass
else:
if self.imageItem.image is not None:
if self.displaymode == DisplayMode.raw:
x = fit2d['centerX']
y = self._raw_image.shape[-2] - fit2d['centerY']
self.centerplot.setData(x=[x], y=[y])
elif self.displaymode == DisplayMode.remesh:
self.centerplot.setData(x=[0], y=[0])
def setGeometry(self, geometry):
super(CenterMarker, self).setGeometry(geometry)
self.drawCenter()
def __init__(self, name):
Node.__init__(self,
name,
terminals={
'x': {
'io': 'in'
},
'y': {
'io': 'in'
},
'color': {
'io': 'in'
},
'plotItem': {
'io': 'out'
}
})
self.ScatterPlotItem = ScatterPlotItem(pen=None,
symbol='o',
size=2,
brush=(255, 255, 255, 160))
self.sigUpdatePlot.connect(self.updatePlot)
class CenterMarker(QSpace):
def __init__(self, *args, **kwargs):
self.centerplot = ScatterPlotItem(brush="r")
self.centerplot.setZValue(100)
super(CenterMarker, self).__init__(*args, **kwargs)
self.addItem(self.centerplot)
self.drawCenter()
def drawCenter(self):
try:
fit2d = self._geometry.getFit2D()
except (TypeError, AttributeError):
pass
else:
x = fit2d['centerX']
y = fit2d['centerY']
self.centerplot.setData(x=[x], y=[y])
def setGeometry(self, geometry):
super(CenterMarker, self).setGeometry(geometry)
self.drawCenter()
def initPlotView(self):
self.plot = PlotWidget(enableAutoRange=True)
self.plot.setXRange(self.lower - self.range * 0.05,
self.upper + self.range * 0.05)
self.plotLegand = self.plot.addLegend()
self.graphicsView.addWidget(self.plot)
self.plotRegion = LinearRegionItem()
self.plotRegion.setZValue(10)
self.peakPoint = ScatterPlotItem(size=8,
pen=mkPen(color='0000FF', width=2),
symbol="+",
brush=mkBrush(255, 255, 255, 240))
self.plot.addItem(self.plotRegion, ignoreBounds=True)
self.plot.addItem(self.peakPoint)
self.setGraphViewStyle()
def __init__(
self,
date_format="%Y-%m-%d %H:%M:%S",
y_format="%0.4f",
trigger_point_size=10,
):
super(DataInspectorLine, self).__init__(angle=90, movable=True)
self._labels = []
self._plot_item = None
self.y_format = y_format
self.trigger_point_size = trigger_point_size
self.date_format = date_format
self._label_style = "background-color: #35393C;"
self.sigPositionChanged.connect(self._inspect)
self._highlights = ScatterPlotItem(
pos=(),
symbol="s",
brush="35393C88",
pxMode=True,
size=trigger_point_size,
)
# hack to make the CurvesPropertiesTool ignore the highlight points
self._highlights._UImodifiable = False
class Masker(QDialog):
"""
An interface for the user to draw masks on an image or movie.
This includes:
- draw masks on the raw image, either by placing discrete vertices
or freestyle drawing
- modify masks by adding / deleting / moving vertices
- change between frames
- export masks
- apply masks to image files
init
----
image_path : str, path to an image file (e.g. ND2 or TIF)
max_points_freestyle : int, the maximum number of points to allow
for a freestyle mask. This limits memory
usage.
parent : root QWidget
"""
def __init__(self,
image_path,
max_points_freestyle=40,
dialog_mode=False,
parent=None):
super(Masker, self).__init__(parent=parent)
self.image_path = image_path
self.max_points_freestyle = max_points_freestyle
self.dialog_mode = dialog_mode
self.initData()
self.initUI()
def initData(self):
"""
Load the images and related data.
"""
# Create the image reader
self.imageReader = ImageReader(self.image_path)
# Get the first image
self.image = self.imageReader.get_frame(0)
def initUI(self):
"""
Initialize the user interface.
"""
# Main layout
L_master = QGridLayout(self)
# An ImageView on the left to contain the subject of masking
self.imageView = ImageView(parent=self)
L_master.addWidget(self.imageView, 0, 0, 15, 2)
self.imageView.setImage(self.image)
# Override the default ImageView.imageItem.mouseClickEvent
self.imageView.imageItem.mouseClickEvent = self._imageView_mouseClickEvent
# Override the default ImageView.imageItem.mouseDoubleClickEvent
self.imageView.imageItem.mouseDoubleClickEvent = \
self._imageView_mouseDoubleClickEvent
# All currently clicked points
self.points = []
# All current PolyLineROI objects
self.polyLineROIs = []
# ScatterPlotItem, to show current accumulated clicks
self.scatterPlotItem = ScatterPlotItem()
self.scatterPlotItem.setParentItem(self.imageView.imageItem)
## WIDGETS
widget_align = Qt.AlignTop
# Frame slider
self.frame_slider = IntSlider(minimum=0,
maximum=self.imageReader.n_frames - 1,
interval=1,
init_value=0,
name='Frame',
parent=self)
L_master.addWidget(self.frame_slider,
0,
2,
1,
1,
alignment=widget_align)
self.frame_slider.assign_callback(self.frame_slider_callback)
# Button: create new ROI
self.create_roi_mode = False
self.B_create_ROI = QPushButton("Draw ROI", parent=self)
self.B_create_ROI.clicked.connect(self.B_create_ROI_callback)
L_master.addWidget(self.B_create_ROI,
10,
2,
1,
1,
alignment=widget_align)
# Button: freestyle drawing to make ROI
self.freestyle_mode = False
self.B_freestyle = QPushButton("Freestyle", parent=self)
self.B_freestyle.clicked.connect(self.B_freestyle_callback)
L_master.addWidget(self.B_freestyle,
11,
2,
1,
1,
alignment=widget_align)
# Pure dialog mode: no options to save or load masks, only
# define and accept
if self.dialog_mode:
# Button: accept the current set of masks. This is only meaningful
# when this class is being used as a dialog by other classes.
self.B_accept = QPushButton("Accept masks", parent=self)
self.B_accept.clicked.connect(self.B_accept_callback)
L_master.addWidget(self.B_accept,
12,
2,
1,
1,
alignment=widget_align)
# Non-dialog mode: full range of options
else:
# Button: apply these masks to the localizations in a file
self.B_apply = QPushButton("Apply masks", parent=self)
self.B_apply.clicked.connect(self.B_apply_callback)
L_master.addWidget(self.B_apply,
12,
2,
1,
1,
alignment=widget_align)
# Button: save masks to a file
self.B_save = QPushButton("Save masks", parent=self)
self.B_save.clicked.connect(self.B_save_callback)
L_master.addWidget(self.B_save,
13,
2,
1,
1,
alignment=widget_align)
# Button: load preexisting masks from a file
self.B_load = QPushButton("Load masks", parent=self)
self.B_load.clicked.connect(self.B_load_callback)
L_master.addWidget(self.B_load,
14,
2,
1,
1,
alignment=widget_align)
# Resize and launch
self.resize(800, 600)
self.show()
## CORE FUNCTIONS
def update_image(self,
frame_index=None,
autoRange=False,
autoLevels=False,
autoHistogramRange=False):
if frame_index is None:
frame_index = self.frame_slider.value()
self.image = self.imageReader.get_frame(frame_index)
self.imageView.setImage(self.image,
autoRange=autoRange,
autoLevels=autoLevels,
autoHistogramRange=autoHistogramRange)
def update_scatter(self):
"""
Write the contents of self.points to self.scatterPlotItem.
"""
self.scatterPlotItem.setData(
pos=np.asarray(self.points),
pxMode=False,
symbol='o',
pen={
'color': '#FFFFFF',
'width': 3.0
},
size=2.0,
brush=None,
)
def clear_scatter(self):
self.points = []
self.scatterPlotItem.setData()
def createPolyLineROI(self, points):
p = PolyLineROI(self.points, closed=True, removable=True)
self.polyLineROIs.append(p)
self.imageView.view.addItem(self.polyLineROIs[-1])
# If the user requests to remove this ROI, remove it
self.polyLineROIs[-1].sigRemoveRequested.connect(self._remove_ROI)
def getPoints(self, polyLineROI):
"""
Return the set of points that make up a PolyLineROI as a
2D ndarray (shape (n_points, 2)).
"""
state = polyLineROI.getState()
return np.asarray([[p.x(), p.y()] for p in state['points']])
def get_currdir(self):
"""
Get the last directory that was accessed by the user. If
no directory was previously accessed, then this is just
the same directory as the image file.
"""
if not hasattr(self, "_currdir"):
self.set_currdir(self.image_path)
return self._currdir
def set_currdir(self, path):
"""
Set the directory returned by self.get_currdir().
args
----
path : str, a file path or directory path. If
a file path, its parent directory is used.
"""
if os.path.isfile(path):
self._currdir = os.path.split(os.path.abspath(path))[0]
elif os.path.isdir(path):
self._currdir = path
def clear_polyLineROIs(self):
"""
Destroy all current PolyLineROI objects.
"""
for p in self.polyLineROIs[::-1]:
self._remove_ROI(p)
## SIGNAL CALLBACKS
def _imageView_mouseClickEvent(self, ev):
if ev.button() == QtCore.Qt.RightButton:
if self.imageView.imageItem.raiseContextMenu(ev):
ev.accept()
if ev.button() == QtCore.Qt.LeftButton and self.create_roi_mode:
self.points.append(ev.pos())
self.update_scatter()
def _imageView_mouseDoubleClickEvent(self, ev):
if self.create_roi_mode:
self.createPolyLineROI(self.points)
self.clear_scatter()
self.create_roi_mode = False
self.imageView.view.state['mouseEnabled'] = np.array([True, True])
elif self.freestyle_mode:
self.B_freestyle_callback()
else:
pass
def _remove_ROI(self, polylineroi):
polylineroi.sigRemoveRequested.disconnect(self._remove_ROI)
self.polyLineROIs.remove(polylineroi)
self.imageView.view.removeItem(polylineroi)
del polylineroi
## WIDGET CALLBACKS
def frame_slider_callback(self):
"""
Callback for user changes to the frame slider, which changes
the current frame shown beneath the masks.
"""
frame_index = self.frame_slider.value()
self.update_image(frame_index=frame_index)
def B_create_ROI_callback(self):
"""
Callback for user selection of the "Draw ROI" button. Enter
create ROI mode, which allows the user to place discrete vertices
sequentially to build a mask.
"""
self.create_roi_mode = True
self.imageView.view.state['mouseEnabled'] = np.array([False, False])
def B_freestyle_callback(self):
"""
Callback for user selection of the "freestyle" button. Enter
freestyle mode, which allows the user to draw a mask on the
image by dragging the mouse.
"""
# End freestyle mode by creating a mask from the drawn points
if self.freestyle_mode:
self.freestyle_mode = False
self.imageView.imageItem.setDrawKernel(kernel=None,
mask=None,
center=None)
mask = (self.image == self.draw_val)
self.points = get_ordered_mask_points(
mask, max_points=self.max_points_freestyle)
self.createPolyLineROI(self.points)
self.frame_slider_callback()
self.points = []
self.B_freestyle.setText("Freestyle")
# Start freestyle mode by enabling drawing on self.imageView.imageItem
else:
self.freestyle_mode = True
self.draw_val = int(self.image.max() + 2)
kernel = np.array([[self.draw_val]])
self.imageView.imageItem.setDrawKernel(kernel=kernel,
mask=None,
center=(0, 0))
self.B_freestyle.setText("Finish freestyle")
def B_save_callback(self):
"""
Save the current set of masks to a file. Every currently
defined mask is saved in a CSV-like format indexed by mask
vertex. This CSV has the following columns:
filename : str, the source filename
mask_index : int, the index of this mask
y : float, the y-coordinate of the vertex
x : float, the x-coordinate of the vertex
vertex : int, the index of this vertex in the
context of its mask
The "vertex" always ascends from 0 to n-1, where n is the number
of vertices in that mask.
"""
# If no masks are defined, do nothing
if len(self.polyLineROIs) == 0:
return
# Prompt the user to select an output filename
out_path = getSaveFilePath(self,
"Select output CSV",
"{}_masks.csv".format(
os.path.splitext(self.image_path)[0]),
"CSV files (*.csv)",
initialdir=self.get_currdir())
# For each PolyLineROI mask, get the corresponding set of vertices
point_arrays = [self.getPoints(p) for p in self.polyLineROIs]
n_masks = len(point_arrays)
# Get the total size of the output dataframe
m = sum([arr.shape[0] for arr in point_arrays])
# Format as a pandas.DataFrame
df = pd.DataFrame(
index=np.arange(m),
columns=["filename", "mask_index", "y", "x", "vertex"])
df["filename"] = self.image_path
c = 0
for mask_index, arr in enumerate(point_arrays):
l = arr.shape[0]
df.loc[c:c + l - 1, "mask_index"] = mask_index
df.loc[c:c + l - 1, "y"] = arr[:, 0]
df.loc[c:c + l - 1, "x"] = arr[:, 1]
df.loc[c:c + l - 1, "vertex"] = np.arange(l)
c += l
# Save
df.to_csv(out_path, index=False)
# Save this directory as the last accessed
self.set_currdir(out_path)
def B_load_callback(self):
"""
Load a set of masks from a file previously saved with this GUI. This
erases any currently defined masks.
"""
# Prompt the user to select a file
path = getOpenFilePath(self,
"Select mask CSV",
"CSV and TIF files (*.csv *.tif *.tiff)",
initialdir=self.get_currdir())
self.set_currdir(path)
ext = os.path.splitext(path)[-1]
# Open this file and check that it contains the necessary info
if ext == ".csv":
try:
df = pd.read_csv(path)
for c in ["filename", "mask_index", "y", "x", "vertex"]:
assert c in df.columns
except:
print("File {} not in the correct format; must be a CSV with " \
"the 'filename', 'mask_index', 'y', 'x', and 'vertex' " \
"columns".format(path))
return
# Warn the user if the image file path in this file doesn't
# match the current image file path
if df.loc[0, "filename"] != self.image_path:
print("WARNING: original file path for this mask file is different " \
"than the current image file.\nOriginal: {}\nCurrent: {}".format(
df.loc[0, "filename"], self.image_path))
elif ext in [".tif", ".tiff"]:
# Load the mask image
masks_im = tifffile.imread(path)
assert len(masks_im.shape) == 2, "WARNING: RGB TIFs not supported"
# Get the set of unique masks defined in this image
n_points = 100
mask_indices = [j for j in list(np.unique(masks_im)) if j != 0]
dfs = []
for mi in mask_indices:
mask_im = masks_im == mi
edges = get_edges(mask_im)
points = get_ordered_mask_points(edges, max_points=n_points)
df = pd.DataFrame(index=list(range(points.shape[0])),
columns=["filename", "mask_index", "y", "x"])
df["filename"] = path
df["mask_index"] = mi
df["y"] = points[:, 0]
df["x"] = points[:, 1]
df["vertex"] = list(range(points.shape[0]))
dfs.append(df)
df = pd.concat(dfs, axis=0, ignore_index=True)
# Erase the current set of masks, if any
self.clear_polyLineROIs()
# Generate a PolyLineROI object for each of the loaded masks
for mask_index, mask_frame in df.groupby("mask_index"):
self.points = np.asarray(mask_frame[["y", "x"]])
self.createPolyLineROI(self.points)
self.points = []
def B_apply_callback(self):
"""
Callback for user selection of the "Apply masks" button. The
user is prompted to select a file containing localizations,
and the localizations in that file are classified according to
which mask they belong to.
"""
# Prompt the user to select a file containing localizations
path = getOpenFilePath(
self,
"Select localization file",
"CSV files and *Tracked.mat files (*.csv *Tracked.mat)",
initialdir=self.get_currdir())
self.set_currdir(path)
# Open this file and make sure it actually contains localizations
ext = os.path.splitext(path)[-1]
try:
if ext == ".csv":
locs = pd.read_csv(path)
assert all([c in locs.columns for c in ['frame', 'y', 'x']])
elif ext == ".mat":
locs = tracked_mat_to_csv(path)
except:
print("Could not load file {}; must either be *.csv or " \
"*Tracked.mat format".format(path))
return
# Prompt the user to input the mask column. This can be something
# as simple as "mask_index", but the user may want something more
# descriptive - like "nuclear_mask" or something. This becomes useful
# when the user applies masks multiple times to the same file - for
# instance, to label primary and secondary features (e.g. nuclei and
# nucleoli) in an image.
col = getTextInputs(["Output mask column name"], ["mask_index"],
title="Select output column name")[0]
# Prompt the user to select a mode for the assignment of trajectories
# to masks. This can either be "by_localization" (independent of the
# trajectory to which each localization is assigned), "single_point"
# (assign all localizations to a mask if a single localization is
# inside the mask), or "all_points" (only assign all localizations to a
# mask if all localizations are inside the mask)
options = ["by_localization", "single_point", "all_points"]
box = SingleComboBoxDialog(
"Method by which trajectories are assigned to masks",
options,
init_value="single_point",
title="Assignment mode",
parent=self)
box.exec_()
if box.Accepted:
mode = box.return_val
else:
print("Dialog not accepted")
return
# Assign each localization to one of the current masks
point_sets = [self.getPoints(p) for p in self.polyLineROIs]
locs[col] = apply_masks(point_sets, locs, mode=mode)
# Save to the same file
if ext == ".csv":
out_path = path
elif ext == ".mat":
if "_Tracked.mat" in path:
out_path = path.replace("_Tracked.mat", ".csv")
elif "Tracked.mat" in path:
out_path = path.replace("Tracked.mat", ".csv")
else:
out_path = "{}.csv".format(os.path.splitext(path)[0])
locs.to_csv(out_path, index=False)
# Save only the masked trajectories to a different file
out_file_inside = "{}_in_mask.csv".format(
os.path.splitext(out_path)[0])
out_file_outside = "{}_outside_mask.csv".format(
os.path.splitext(out_path)[0])
locs[locs["mask_index"] > 0].to_csv(out_file_inside, index=False)
locs[locs["mask_index"] == 0].to_csv(out_file_outside, index=False)
# Show the result
show_mask_assignments(point_sets,
locs,
mask_col=col,
max_points_scatter=5000)
def B_accept_callback(self):
"""
If this GUI is being used as a dialog, accept and return the currently
defined set of masks.
"""
self.return_val = [self.getPoints(p) for p in self.polyLineROIs]
print(self.return_val)
self.accept()
def initUI(self):
"""
Initialize the user interface.
"""
# Main layout
L_master = QGridLayout(self)
# An ImageView on the left to contain the subject of masking
self.imageView = ImageView(parent=self)
L_master.addWidget(self.imageView, 0, 0, 15, 2)
self.imageView.setImage(self.image)
# Override the default ImageView.imageItem.mouseClickEvent
self.imageView.imageItem.mouseClickEvent = self._imageView_mouseClickEvent
# Override the default ImageView.imageItem.mouseDoubleClickEvent
self.imageView.imageItem.mouseDoubleClickEvent = \
self._imageView_mouseDoubleClickEvent
# All currently clicked points
self.points = []
# All current PolyLineROI objects
self.polyLineROIs = []
# ScatterPlotItem, to show current accumulated clicks
self.scatterPlotItem = ScatterPlotItem()
self.scatterPlotItem.setParentItem(self.imageView.imageItem)
## WIDGETS
widget_align = Qt.AlignTop
# Frame slider
self.frame_slider = IntSlider(minimum=0,
maximum=self.imageReader.n_frames - 1,
interval=1,
init_value=0,
name='Frame',
parent=self)
L_master.addWidget(self.frame_slider,
0,
2,
1,
1,
alignment=widget_align)
self.frame_slider.assign_callback(self.frame_slider_callback)
# Button: create new ROI
self.create_roi_mode = False
self.B_create_ROI = QPushButton("Draw ROI", parent=self)
self.B_create_ROI.clicked.connect(self.B_create_ROI_callback)
L_master.addWidget(self.B_create_ROI,
10,
2,
1,
1,
alignment=widget_align)
# Button: freestyle drawing to make ROI
self.freestyle_mode = False
self.B_freestyle = QPushButton("Freestyle", parent=self)
self.B_freestyle.clicked.connect(self.B_freestyle_callback)
L_master.addWidget(self.B_freestyle,
11,
2,
1,
1,
alignment=widget_align)
# Pure dialog mode: no options to save or load masks, only
# define and accept
if self.dialog_mode:
# Button: accept the current set of masks. This is only meaningful
# when this class is being used as a dialog by other classes.
self.B_accept = QPushButton("Accept masks", parent=self)
self.B_accept.clicked.connect(self.B_accept_callback)
L_master.addWidget(self.B_accept,
12,
2,
1,
1,
alignment=widget_align)
# Non-dialog mode: full range of options
else:
# Button: apply these masks to the localizations in a file
self.B_apply = QPushButton("Apply masks", parent=self)
self.B_apply.clicked.connect(self.B_apply_callback)
L_master.addWidget(self.B_apply,
12,
2,
1,
1,
alignment=widget_align)
# Button: save masks to a file
self.B_save = QPushButton("Save masks", parent=self)
self.B_save.clicked.connect(self.B_save_callback)
L_master.addWidget(self.B_save,
13,
2,
1,
1,
alignment=widget_align)
# Button: load preexisting masks from a file
self.B_load = QPushButton("Load masks", parent=self)
self.B_load.clicked.connect(self.B_load_callback)
L_master.addWidget(self.B_load,
14,
2,
1,
1,
alignment=widget_align)
# Resize and launch
self.resize(800, 600)
self.show()
def __init__(self, settings, server):
super().__init__()
self.server = server
self.timer = QTimer()
self.timer.timeout.connect(self.time_tick)
self.settings = settings
self.current_class = None
self.current_students = []
self.stack = QStackedLayout()
self.setLayout(self.stack)
# First page: connection instructions
connect_widget = QWidget()
connect_layout = QVBoxLayout(connect_widget)
connect_layout.addStretch()
connect_label = QLabel(
"Open a world in Minecraft, open a terminal (press t), and type:",
self)
connect_layout.addWidget(connect_label)
self.connect_command = f'/connect {server.get_ip()}:{PORT}'
connect_command_box = QLineEdit(self.connect_command, self)
connect_command_box.setReadOnly(True)
connect_layout.addWidget(connect_command_box)
connect_copy_button = QPushButton("Copy to Clipboard", self)
connect_copy_button.clicked.connect(
lambda: QApplication.clipboard().setText(self.connect_command))
connect_layout.addWidget(connect_copy_button)
connection_problems_button = QPushButton("Connection Problems?", self)
connection_problems_button.clicked.connect(self.show_connection_help)
connect_layout.addWidget(connection_problems_button)
connect_layout.addStretch()
self.stack.addWidget(connect_widget)
# Main page
main_col_widget = QWidget()
columns = QHBoxLayout(main_col_widget)
col_left = QVBoxLayout()
col_mid = QVBoxLayout()
col_right = QVBoxLayout()
columns.addLayout(col_left)
columns.addSpacing(10)
columns.addLayout(col_mid)
columns.addSpacing(10)
columns.addLayout(col_right)
self.stack.addWidget(main_col_widget)
self.pause_button = self.setup_toggle_button(col_left,
self.server.pause_game,
'Un-pause',
self.server.unpause_game,
'Pause')
button_size = self.pause_button.size()
self.disable_chat_button = self.setup_toggle_button(
col_left, self.server.disable_chat, 'Enable Chat',
self.server.enable_chat, 'Disable Chat', button_size)
self.allow_mobs_button = self.setup_toggle_button(
col_left, self.server.disallow_mobs, 'Allow Mobs',
self.server.allow_mobs, 'Disable Mobs', button_size)
self.allow_destructiveobjects_button = self.setup_toggle_button(
col_left, self.server.disallow_destructiveobjects,
'Enable Destructive Items', self.server.allow_destructiveobjects,
'Disable Destructive Items', button_size)
self.allow_player_damage_button = self.setup_toggle_button(
col_left, self.server.disallow_player_damage,
'Enable Player Damage', self.server.allow_player_damage,
'Disable Player Damage', button_size)
self.allow_pvp_button = self.setup_toggle_button(
col_left, self.server.disallow_pvp, 'Allow Player Fighting',
self.server.allow_pvp, 'Disable Player Fighting', button_size)
self.immutable_button = self.setup_toggle_button(
col_left, self.server.immutable_world,
'Enable World Modifications', self.server.mutable_world,
'Disable World Modifications', button_size)
self.weather_button = self.setup_toggle_button(
col_left, self.server.perfect_weather, 'Disable Perfect Weather',
self.server.imperfect_weather, 'Enable Perfect Weather',
button_size)
self.disable_potions_button = self.setup_toggle_button(
col_left, self.server.disable_potions, 'Enable Potions',
self.server.enable_potions, 'Disable Potions', button_size)
# self.clear_potions_button = QPushButton('Clear All Potion Effects', self)
# self.clear_potions_button.resize(button_size)
# self.clear_potions_button.clicked.connect(lambda: self.server.clear_effects("@a"))
# col_left.addWidget(self.clear_potions_button)
self.teleport_button = QPushButton('Teleport Everyone to You', self)
self.teleport_button.resize(button_size)
self.teleport_button.clicked.connect(
lambda: self.server.teleport_all_to("@s"))
col_left.addWidget(self.teleport_button)
self.disconnect_button = QPushButton('Disconnect', self)
self.disconnect_button.resize(button_size)
self.disconnect_button.clicked.connect(self.server.socket_disconnected)
col_left.addWidget(self.disconnect_button)
col_left.addStretch()
self.version_label = QLabel(f'Version {VERSION}', self)
self.version_label.setAlignment(Qt.AlignCenter)
col_left.addWidget(self.version_label)
self.feedback_button = QPushButton('Feedback/Bug report', self)
self.feedback_button.resize(button_size)
self.feedback_button.clicked.connect(
lambda: QDesktopServices.openUrl(FEEDBACK_URL))
col_left.addWidget(self.feedback_button)
# Middle Column: Roll/Register
self.classes_combo = QComboBox(self)
class_names = self.settings.value("class_names", [])
self.classes_combo.addItem("Select class")
self.classes_combo.addItem("Add a class")
self.classes_combo.addItem("Delete a class")
self.classes_combo.addItems(class_names)
self.classes_combo.currentTextChanged.connect(self.class_changed)
col_mid.addWidget(self.classes_combo)
self.users_table = QTableWidget(0, 2)
self.users_table.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.users_table.setSizePolicy(
QSizePolicy(QSizePolicy.Minimum, QSizePolicy.MinimumExpanding))
self.users_table.setFixedWidth(140)
self.users_table.verticalHeader().hide()
header = self.users_table.horizontalHeader()
header.setSectionResizeMode(0, QHeaderView.Stretch)
header.setSectionResizeMode(1, QHeaderView.ResizeToContents)
header.hide()
col_mid.addWidget(self.users_table)
self.class_edit_button = QPushButton("Edit Class", self)
col_mid.addWidget(self.class_edit_button)
self.class_edit_button.clicked.connect(self.edit_class)
self.chat_box = QPlainTextEdit(
f'Minecraft Education Chat Logs {datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")}',
self)
self.chat_box.setReadOnly(True)
col_right.addWidget(self.chat_box)
self.chat_input = QLineEdit(self)
self.chat_input.setPlaceholderText("Type chat here; enter to send")
self.chat_input.returnPressed.connect(self.chat_enter)
col_right.addWidget(self.chat_input)
self.chat_save = QPushButton("Save Chat Logs", self)
self.chat_save.clicked.connect(self.save_chat)
col_right.addWidget(self.chat_save)
self.user_map = PlotWidget()
self.map_item = ScatterPlotItem(size=10)
self.user_map.addItem(self.map_item)
self.user_map.getPlotItem().hideAxis('left')
self.user_map.getPlotItem().hideAxis('bottom')
self.map_item.scene().sigMouseMoved.connect(self.map_hover)
map_viewbox = self.map_item.getViewBox()
map_viewbox.menu = None
col_right.addWidget(self.user_map)
self.user_map_info = QLineEdit("Hover over a user", self)
self.user_map_info.setReadOnly(True)
col_right.addWidget(self.user_map_info)
self.setGeometry(300, 300, 800, 600)
self.setWindowTitle('MineClass')
self.stack.setCurrentIndex(0)
self.activate_buttons(False)
self.show()
if is_newer_version_available():
QMessageBox.about(
self, "Newer Version Available",
f'A newer version of this program is available <a href="{GITHUB_DOWNLOAD_URL}">here</a>.'
)
if not self.settings.value("HasRunFirstTime", False):
self.show_connection_help()
self.settings.setValue("HasRunFirstTime", True)
class MCClassroom(QWidget):
def __init__(self, settings, server):
super().__init__()
self.server = server
self.timer = QTimer()
self.timer.timeout.connect(self.time_tick)
self.settings = settings
self.current_class = None
self.current_students = []
self.stack = QStackedLayout()
self.setLayout(self.stack)
# First page: connection instructions
connect_widget = QWidget()
connect_layout = QVBoxLayout(connect_widget)
connect_layout.addStretch()
connect_label = QLabel(
"Open a world in Minecraft, open a terminal (press t), and type:",
self)
connect_layout.addWidget(connect_label)
self.connect_command = f'/connect {server.get_ip()}:{PORT}'
connect_command_box = QLineEdit(self.connect_command, self)
connect_command_box.setReadOnly(True)
connect_layout.addWidget(connect_command_box)
connect_copy_button = QPushButton("Copy to Clipboard", self)
connect_copy_button.clicked.connect(
lambda: QApplication.clipboard().setText(self.connect_command))
connect_layout.addWidget(connect_copy_button)
connection_problems_button = QPushButton("Connection Problems?", self)
connection_problems_button.clicked.connect(self.show_connection_help)
connect_layout.addWidget(connection_problems_button)
connect_layout.addStretch()
self.stack.addWidget(connect_widget)
# Main page
main_col_widget = QWidget()
columns = QHBoxLayout(main_col_widget)
col_left = QVBoxLayout()
col_mid = QVBoxLayout()
col_right = QVBoxLayout()
columns.addLayout(col_left)
columns.addSpacing(10)
columns.addLayout(col_mid)
columns.addSpacing(10)
columns.addLayout(col_right)
self.stack.addWidget(main_col_widget)
self.pause_button = self.setup_toggle_button(col_left,
self.server.pause_game,
'Un-pause',
self.server.unpause_game,
'Pause')
button_size = self.pause_button.size()
self.disable_chat_button = self.setup_toggle_button(
col_left, self.server.disable_chat, 'Enable Chat',
self.server.enable_chat, 'Disable Chat', button_size)
self.allow_mobs_button = self.setup_toggle_button(
col_left, self.server.disallow_mobs, 'Allow Mobs',
self.server.allow_mobs, 'Disable Mobs', button_size)
self.allow_destructiveobjects_button = self.setup_toggle_button(
col_left, self.server.disallow_destructiveobjects,
'Enable Destructive Items', self.server.allow_destructiveobjects,
'Disable Destructive Items', button_size)
self.allow_player_damage_button = self.setup_toggle_button(
col_left, self.server.disallow_player_damage,
'Enable Player Damage', self.server.allow_player_damage,
'Disable Player Damage', button_size)
self.allow_pvp_button = self.setup_toggle_button(
col_left, self.server.disallow_pvp, 'Allow Player Fighting',
self.server.allow_pvp, 'Disable Player Fighting', button_size)
self.immutable_button = self.setup_toggle_button(
col_left, self.server.immutable_world,
'Enable World Modifications', self.server.mutable_world,
'Disable World Modifications', button_size)
self.weather_button = self.setup_toggle_button(
col_left, self.server.perfect_weather, 'Disable Perfect Weather',
self.server.imperfect_weather, 'Enable Perfect Weather',
button_size)
self.disable_potions_button = self.setup_toggle_button(
col_left, self.server.disable_potions, 'Enable Potions',
self.server.enable_potions, 'Disable Potions', button_size)
# self.clear_potions_button = QPushButton('Clear All Potion Effects', self)
# self.clear_potions_button.resize(button_size)
# self.clear_potions_button.clicked.connect(lambda: self.server.clear_effects("@a"))
# col_left.addWidget(self.clear_potions_button)
self.teleport_button = QPushButton('Teleport Everyone to You', self)
self.teleport_button.resize(button_size)
self.teleport_button.clicked.connect(
lambda: self.server.teleport_all_to("@s"))
col_left.addWidget(self.teleport_button)
self.disconnect_button = QPushButton('Disconnect', self)
self.disconnect_button.resize(button_size)
self.disconnect_button.clicked.connect(self.server.socket_disconnected)
col_left.addWidget(self.disconnect_button)
col_left.addStretch()
self.version_label = QLabel(f'Version {VERSION}', self)
self.version_label.setAlignment(Qt.AlignCenter)
col_left.addWidget(self.version_label)
self.feedback_button = QPushButton('Feedback/Bug report', self)
self.feedback_button.resize(button_size)
self.feedback_button.clicked.connect(
lambda: QDesktopServices.openUrl(FEEDBACK_URL))
col_left.addWidget(self.feedback_button)
# Middle Column: Roll/Register
self.classes_combo = QComboBox(self)
class_names = self.settings.value("class_names", [])
self.classes_combo.addItem("Select class")
self.classes_combo.addItem("Add a class")
self.classes_combo.addItem("Delete a class")
self.classes_combo.addItems(class_names)
self.classes_combo.currentTextChanged.connect(self.class_changed)
col_mid.addWidget(self.classes_combo)
self.users_table = QTableWidget(0, 2)
self.users_table.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.users_table.setSizePolicy(
QSizePolicy(QSizePolicy.Minimum, QSizePolicy.MinimumExpanding))
self.users_table.setFixedWidth(140)
self.users_table.verticalHeader().hide()
header = self.users_table.horizontalHeader()
header.setSectionResizeMode(0, QHeaderView.Stretch)
header.setSectionResizeMode(1, QHeaderView.ResizeToContents)
header.hide()
col_mid.addWidget(self.users_table)
self.class_edit_button = QPushButton("Edit Class", self)
col_mid.addWidget(self.class_edit_button)
self.class_edit_button.clicked.connect(self.edit_class)
self.chat_box = QPlainTextEdit(
f'Minecraft Education Chat Logs {datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")}',
self)
self.chat_box.setReadOnly(True)
col_right.addWidget(self.chat_box)
self.chat_input = QLineEdit(self)
self.chat_input.setPlaceholderText("Type chat here; enter to send")
self.chat_input.returnPressed.connect(self.chat_enter)
col_right.addWidget(self.chat_input)
self.chat_save = QPushButton("Save Chat Logs", self)
self.chat_save.clicked.connect(self.save_chat)
col_right.addWidget(self.chat_save)
self.user_map = PlotWidget()
self.map_item = ScatterPlotItem(size=10)
self.user_map.addItem(self.map_item)
self.user_map.getPlotItem().hideAxis('left')
self.user_map.getPlotItem().hideAxis('bottom')
self.map_item.scene().sigMouseMoved.connect(self.map_hover)
map_viewbox = self.map_item.getViewBox()
map_viewbox.menu = None
col_right.addWidget(self.user_map)
self.user_map_info = QLineEdit("Hover over a user", self)
self.user_map_info.setReadOnly(True)
col_right.addWidget(self.user_map_info)
self.setGeometry(300, 300, 800, 600)
self.setWindowTitle('MineClass')
self.stack.setCurrentIndex(0)
self.activate_buttons(False)
self.show()
if is_newer_version_available():
QMessageBox.about(
self, "Newer Version Available",
f'A newer version of this program is available <a href="{GITHUB_DOWNLOAD_URL}">here</a>.'
)
if not self.settings.value("HasRunFirstTime", False):
self.show_connection_help()
self.settings.setValue("HasRunFirstTime", True)
def show_connection_help(self):
QMessageBox.about(
self, "Connection Help",
'''Before using (or if Minecraft has been newly installed), go to Settings->Profile and disable "Require Encrypted Websockets"\n\n
Sometimes you'll need to attempt connecting twice (use the up arrow in the Minecraft terminal to access history'''
)
def save_chat(self):
options = QFileDialog.Options()
file_name, _ = QFileDialog.getSaveFileName(
self,
"Save Chat Logs",
"",
"Text Files (*.txt);;All Files (*)",
options=options)
if file_name:
with open(file_name, "w") as f:
f.write(self.chat_box.toPlainText())
def chat_enter(self):
server.send_chat(self.chat_input.text())
self.update_chat_box("Teacher", self.chat_input.text(), "chat")
self.chat_input.clear()
def map_hover(self, pos):
act_pos = self.map_item.mapFromScene(pos)
points = self.map_item.pointsAt(act_pos)
text = ""
for p in points:
text += f'{p.data()}: ({round(p.pos()[0])}, {round(p.pos()[1])}), '
self.user_map_info.setText(text)
def time_tick(self):
self.server.get_users()
def start_timer(self):
self.time_tick()
self.timer.start(10000)
def stop_timer(self):
self.timer.stop()
def update_chat_box(self, sender, message, message_type, receiver=None):
t = datetime.datetime.now().strftime("%H:%M:%S")
if message_type == "chat":
out = f'{t} <{sender}> {message}'
elif message_type == "tell":
out = f'{t} <{sender} whispers to {receiver}> {message}'
self.chat_box.appendPlainText(out)
def activate_buttons(self, activate):
self.pause_button.setDisabled(not activate)
def setup_toggle_button(self,
parent,
checked_action,
checked_text,
unchecked_action,
unchecked_text,
size=None):
button = QPushButton(unchecked_text, self)
button.resize(button.sizeHint() if size is None else size)
button.setCheckable(True)
parent.addWidget(button)
def toggle_button_clicked(checked_status):
if checked_status:
checked_action()
button.setText(checked_text)
else:
unchecked_action()
button.setText(unchecked_text)
button.toggled.connect(toggle_button_clicked)
return button
def get_students_from_grid(self):
try:
return [
self.users_table.item(i, 0).text()
for i in range(self.users_table.rowCount())
]
except AttributeError:
return []
def edit_class(self):
selection = self.classes_combo.currentText()
if selection in ("Select class", "Add a class"):
QMessageBox.about(self, "Error",
"Please select (or create) a class first")
return
current_list = self.get_students_from_grid()
new_list, ok_pressed = QInputDialog().getMultiLineText(
self,
"Edit Class List",
"Add or remove students from this class",
text="\n".join(current_list))
if ok_pressed:
students = [i for i in new_list.split("\n")
if i] # list comprehension to remove empty strings
self.current_students = students
self.settings.setValue(f'classes/{self.current_class}', students)
self.load_users()
def class_changed(self):
selection = self.classes_combo.currentText()
# if selection != "Select class":
# self.classes_combo.removeItem(self.classes_combo.findText("Select class"))
if selection == "Add a class":
new_class, ok_pressed = QInputDialog.getText(
self, 'Class Name', 'Enter the Class Name or Code')
if ok_pressed:
classes = self.settings.value('class_names', [])
if new_class in classes:
print('Class already exists; ignoring')
else:
classes.append(new_class)
self.settings.setValue('class_names', classes)
self.classes_combo.addItem(new_class)
self.classes_combo.setCurrentIndex(
self.classes_combo.findText(new_class))
elif selection == "Select class":
pass
elif selection == "Delete a class":
current_classes = self.settings.value('class_names', [])
if current_classes:
class_to_delete, ok_pressed = QInputDialog.getItem(
self, 'Delete Class', 'Select which class to delete',
current_classes, 0, False)
if ok_pressed and class_to_delete:
current_classes.remove(class_to_delete)
self.settings.setValue('class_names', current_classes)
self.settings.remove(f'classes/{class_to_delete}')
self.classes_combo.removeItem(
self.classes_combo.findText(class_to_delete))
#TODO delete stdents from table
self.current_class = None
self.current_students = []
else:
QMessageBox.information(self, "No Classes!",
"No Class to delete!")
self.classes_combo.setCurrentIndex(0)
else:
self.current_class = selection
self.current_students = self.settings.value(
f'classes/{selection}', [])
self.load_users()
def load_users(self):
if len(self.current_students) != self.users_table.rowCount():
self.users_table.setRowCount(len(self.current_students))
for i, user in enumerate(self.current_students):
self.users_table.setItem(i, 0, QTableWidgetItem(user))
self.users_table.sortItems(0, QtCore.Qt.AscendingOrder)
self.users_table.sortItems(1, QtCore.Qt.DescendingOrder)
def update_users_from_mc(self, users):
table_user_count = self.users_table.rowCount()
for i in range(table_user_count):
current_table_user = self.users_table.item(i, 0).text()
if current_table_user in users:
tick = QTableWidgetItem("✓")
tick.setTextAlignment(QtCore.Qt.AlignCenter)
tick.setBackground(QColor(QtCore.Qt.green))
self.users_table.setItem(i, 1, tick)
users.remove(current_table_user)
else:
cross = QTableWidgetItem("✗")
cross.setTextAlignment(QtCore.Qt.AlignCenter)
cross.setBackground(QColor(QtCore.Qt.red))
self.users_table.setItem(i, 1, cross)
#handle users from server but not in table
self.users_table.setRowCount(table_user_count + len(users))
for i, user in enumerate(users):
self.users_table.setItem(i + table_user_count, 0,
QTableWidgetItem(user))
self.users_table.sortItems(0, QtCore.Qt.AscendingOrder)
self.users_table.sortItems(1, QtCore.Qt.DescendingOrder)
self.users_table.resizeRowsToContents()
def update_map(self, users):
data = [
{
'pos': (int(u['position']['x']), int(u['position']['z'])),
'data': u['name'],
'brush': mkBrush(
'g'
), #mkBrush("r" if u['name'] == self.server.self_name else "g"),
'symbol': ("s" if u['name'] == self.server.self_name else "o"),
} for u in users.values()
]
self.map_item.setData(data)
def __init__(self, imodel, iview, geom, parent=None):
QObject.__init__(self, parent)
self.imodel = imodel
self.dmodel = imodel.model
self.iview = iview
self.iview.ui.menuBtn.hide()
self.iview.ui.roiBtn.hide()
# Thanks CXIVIEW, Anton & Valerio
pos = np.array([0.0, 0.5, 1.0])
color = np.array(
[[255, 255, 255, 255], [128, 128, 128, 255], [0, 0, 0, 255]],
dtype=np.ubyte)
new_color_map = ColorMap(pos, color)
self.iview.ui.histogram.gradient.setColorMap(new_color_map)
self.lastrow = -1
self.curFileName = None
self.curFile = None
self.canDraw = self.dmodel.canSaveLst()
self.checkEvent = "event" in self.dmodel.cols
self.yxmap = None
self.slab_shape = None
self.img_shape = None
self.geom_coffset = 0
self.geom_pixsize = None
self.im_out = None
self.resolutionLambda = None
self.pixRadiusToRes = None
self.hkl = None
self.hklLookup = None
self.imodel.dataChanged.connect(self.draw)
self.iview.view.menu.addSeparator()
openGeomAct = self.iview.view.menu.addAction("Load CrystFEL Geometry")
openGeomAct.triggered.connect(self.openGeom)
peakmenu = self.iview.view.menu.addMenu("Peaks")
self.peakActionGroup = QActionGroup(self)
self.peakActionGroup.setExclusive(True)
self.peakActionGroup.triggered.connect(self.drawPeaks)
peakNone = peakmenu.addAction("None")
peakNone.setCheckable(True)
peakNone.setChecked(True)
peakNone.setData(0)
self.peakActionGroup.addAction(peakNone)
peakCXI = peakmenu.addAction("CXI")
peakCXI.setCheckable(True)
peakCXI.setEnabled(self.dmodel.canSaveLst())
peakCXI.setData(1)
self.peakActionGroup.addAction(peakCXI)
peakStream = peakmenu.addAction("Stream")
peakStream.setCheckable(True)
peakStream.setEnabled(self.dmodel.hasStreamPeaks())
peakStream.setData(2)
self.peakActionGroup.addAction(peakStream)
self.peakCanvas = ScatterPlotItem()
self.iview.getView().addItem(self.peakCanvas)
reflectionmenu = self.iview.view.menu.addMenu("Reflections")
self.reflectionActionGroup = QActionGroup(self)
self.reflectionActionGroup.setExclusive(True)
self.reflectionActionGroup.triggered.connect(self.drawReflections)
refNone = reflectionmenu.addAction("None")
refNone.setCheckable(True)
refNone.setChecked(True)
refNone.setData(0)
self.reflectionActionGroup.addAction(refNone)
refStream = reflectionmenu.addAction("Stream")
refStream.setCheckable(True)
refStream.setEnabled(self.dmodel.hasStreamReflections())
refStream.setData(1)
self.reflectionActionGroup.addAction(refStream)
self.reflectionCanvas = ScatterPlotItem()
self.iview.getView().addItem(self.reflectionCanvas)
self.drawResRingsAct = self.iview.view.menu.addAction(
"Resolution Rings")
self.drawResRingsAct.setCheckable(True)
self.drawResRingsAct.setChecked(False)
self.drawResRingsAct.triggered.connect(self.drawResRings)
self.drawResRingsAct.setEnabled(self.yxmap is not None)
self.resolutionRingsCanvas = ScatterPlotItem()
self.iview.getView().addItem(self.resolutionRingsCanvas)
self.resRingsTextItems = []
for x in self.dmodel.cfg.viewerResolutionRingsAngstroms:
self.resRingsTextItems.append(TextItem('', anchor=(0.5, 0.8)))
self.iview.getView().addItem(self.resRingsTextItems[-1])
self.drawResolutionLimitAct = self.iview.view.menu.addAction(
"Resolution Limit Ring")
self.drawResolutionLimitAct.setCheckable(True)
self.drawResolutionLimitAct.setChecked(False)
self.drawResolutionLimitAct.triggered.connect(self.drawResLimitRing)
self.drawResolutionLimitAct.setEnabled(
self.yxmap is not None and 'reslim' in self.dmodel.cols)
self.resolutionLimitCanvas = ScatterPlotItem()
self.iview.getView().addItem(self.resolutionLimitCanvas)
if geom is not None:
self.loadGeom(geom)
self.toolTipsAct = self.iview.view.menu.addAction(
"Show Position in Tool Tip")
self.toolTipsAct.setCheckable(True)
self.toolTipsAct.setChecked(True)
self.iview.scene.sigMouseMoved.connect(self.mouseMove)
self.draw()
def initUI(self):
# Master layout
self.win = QWidget()
L_master = QGridLayout(self.win)
# Left subwindow, for widgets
win_left = QWidget(self.win)
L_left = QGridLayout(win_left)
L_master.addWidget(win_left, 0, 0, 1, 3)
# Right subwindow, for images
win_right = QWidget(self.win)
L_right = QGridLayout(win_right)
L_master.addWidget(win_right, 0, 3, 1, 1)
# Add four LabeledImageViews to this window
liv_labels = ['(1) Raw', '(2) Filtered', '(3) Convolved', '(4) Binary']
self.LIVs = [LabeledImageView(parent=win_left, label=liv_labels[j]) \
for j in range(4)]
for j in range(4):
L_left.addWidget(self.LIVs[j], j % 2, j // 2)
self.LIVs[j].setImage(self.images[j])
# Link the views between the ImageViews
for j in range(1, 4):
self.LIVs[j].ImageView.view.setXLink(self.LIVs[0].ImageView.view)
self.LIVs[j].ImageView.view.setYLink(self.LIVs[0].ImageView.view)
# Set up three ScatterPlotItems for each of the first three ImageViews,
# for overlaying detections as symbols
self.SPIs = [ScatterPlotItem() for j in range(3)]
for i in range(3):
self.SPIs[i].setParentItem(self.LIVs[i].ImageView.imageItem)
## WIDGETS
widget_align = Qt.AlignTop
slider_min_width = 125
# Frame slider
self.frame_slider = IntSlider(minimum=self.start_frame,
maximum=self.stop_frame,
interval=1,
name='Frame',
init_value=0,
min_width=slider_min_width,
parent=win_right)
L_right.addWidget(self.frame_slider, 0, 0, alignment=widget_align)
self.frame_slider.assign_callback(self.frame_slider_callback)
# Select filtering method
filter_methods = keys_to_str(FILTER_SLIDER_CONFIG.keys())
self.M_filter = LabeledQComboBox(filter_methods,
"Filter method",
init_value="identity",
parent=win_right)
L_right.addWidget(self.M_filter, 1, 0, alignment=widget_align)
self.M_filter.assign_callback(self.M_filter_callback)
# Select filtering chunk size
chunk_size_choices = [
str(i) for i in [2, 5, 10, 15, 20, 30, 40, 60, 80, 100, 200]
]
self.M_chunk_size = LabeledQComboBox(chunk_size_choices, "Chunk size")
L_right.addWidget(self.M_chunk_size, 2, 0, alignment=widget_align)
self.M_chunk_size.assign_callback(self.M_chunk_size_callback)
self.M_chunk_size.setCurrentText(str(self.ChunkFilter.chunk_size))
# Three semantically-flexible filtering FloatSliders
self.filter_sliders = [
FloatSlider(parent=win_right, min_width=slider_min_width)
for j in range(3)
]
for i in range(len(self.filter_sliders)):
L_right.addWidget(self.filter_sliders[i],
i + 3,
0,
alignment=widget_align)
self.filter_sliders[i].assign_callback(
getattr(self, "filter_slider_%d_callback" % i))
self.filter_sliders[i].hide()
# Button to change ROI
self.B_change_roi = QPushButton("Change ROI", win_right)
L_right.addWidget(self.B_change_roi, 6, 0, alignment=widget_align)
self.B_change_roi.clicked.connect(self.B_change_roi_callback)
# Button to change frame range
self.B_change_frame_range = QPushButton("Change frame range",
win_right)
L_right.addWidget(self.B_change_frame_range,
7,
0,
alignment=widget_align)
self.B_change_frame_range.clicked.connect(
self.B_change_frame_range_callback)
# Select detection method
detect_methods = keys_to_str(DETECT_SLIDER_CONFIG.keys())
self.M_detect = LabeledQComboBox(detect_methods,
"Detect method",
init_value="llr",
parent=win_right)
L_right.addWidget(self.M_detect, 0, 1, alignment=widget_align)
# Set the initial detection method and arguments
init_detect_method = 'llr'
self.M_detect.setCurrentText(init_detect_method)
self.detect_kwargs = {DETECT_SLIDER_CONFIG[init_detect_method][i]['name']: \
DETECT_SLIDER_CONFIG[init_detect_method][i]['init_value'] \
for i in DETECT_SLIDER_CONFIG[init_detect_method].keys()}
self.detect_kwargs['method'] = init_detect_method
self.M_detect.assign_callback(self.M_detect_callback)
# Four semantically-flexible detection FloatSliders
self.detect_sliders = [
FloatSlider(parent=win_right, min_width=slider_min_width)
for j in range(4)
]
for i in range(len(self.detect_sliders)):
L_right.addWidget(self.detect_sliders[i],
i + 1,
1,
alignment=widget_align)
self.detect_sliders[i].assign_callback(
getattr(self, "detect_slider_%d_callback" % i))
# Autoscale the detection threshold
self.B_auto_threshold = QPushButton("Rescale threshold",
parent=win_right)
L_right.addWidget(self.B_auto_threshold, 6, 1, alignment=widget_align)
self.B_auto_threshold.clicked.connect(self.B_auto_threshold_callback)
# Overlay detections as symbols
self.B_spot_overlay_state = False
self.B_spot_overlay = QPushButton("Overlay detections",
parent=win_right)
L_right.addWidget(self.B_spot_overlay, 7, 1, alignment=widget_align)
self.B_spot_overlay.clicked.connect(self.B_spot_overlay_callback)
# Change the symbol used for spot overlays
symbol_choices = ['+', 'o', 'open +']
self.M_symbol = LabeledQComboBox(symbol_choices,
"Spot symbol",
init_value='o',
parent=win_right)
L_right.addWidget(self.M_symbol, 5, 1, alignment=widget_align)
self.M_symbol.assign_callback(self.M_symbol_callback)
# Save result to file
self.B_save = QPushButton("Save settings", parent=win_right)
L_right.addWidget(self.B_save, 8, 1, alignment=widget_align)
self.B_save.clicked.connect(self.B_save_callback)
# Show individual spots
self.B_show_spots = QPushButton("Show individual spots",
parent=win_right)
L_right.addWidget(self.B_show_spots, 9, 1, alignment=widget_align)
self.B_show_spots.clicked.connect(self.B_show_spots_callback)
## EMPTY WIDGETS
for j in range(8, 24):
_ql = QLabel(win_right)
L_right.addWidget(_ql, j, 0, alignment=widget_align)
## KEYBOARD SHORTCUTS - tab right/left through frames
self.left_shortcut = QShortcut(QKeySequence(QtGui_Qt.Key_Left),
self.win)
self.right_shortcut = QShortcut(QKeySequence(QtGui_Qt.Key_Right),
self.win)
self.left_shortcut.activated.connect(self.tab_prev_frame)
self.right_shortcut.activated.connect(self.tab_next_frame)
## INITIALIZATION
self.change_detect_method(init_detect_method)
self.filter()
self.detect()
self.auto_threshold()
self.update_images(1,
2,
3,
autoRange=True,
autoLevels=True,
autoHistogramRange=True)
# Resize GUI
self.win.resize(self.gui_width, self.gui_height)
# Show the main window
self.win.show()
def setupLayout(self):
self.layout = QHBoxLayout(self)
self.splitter = QSplitter(Qt.Horizontal)
self.settingswidget = QWidget(self)
self.settingswidget.setMaximumWidth(400)
self.settingslayout = QVBoxLayout()
self.percolationWidget = PercolationWidget()
self.graph_type_combobox = QComboBox(self)
self.graph_type_combobox.addItems(self.graph_names)
self.graph_type_combobox.currentIndexChanged.connect(
self.handleGraphTypeChanged)
self.graph_type_combobox.setFocusPolicy(Qt.NoFocus)
self.settingslayout.addWidget(self.graph_type_combobox)
self.p_slider_layout = QHBoxLayout()
self.settingslayout.addLayout(self.p_slider_layout)
self.p_slider_layout.addWidget(QLabel("Set p value: ", self))
self.p_slider_label = QLabel(self)
self.p_slider = QSlider(Qt.Horizontal, self)
self.p_slider.valueChanged.connect(self.handlePSliderChange)
self.p_slider_layout.addWidget(self.p_slider)
self.p_slider_layout.addWidget(self.p_slider_label)
self.N_slider_layout = QHBoxLayout()
self.settingslayout.addLayout(self.N_slider_layout)
self.N_slider_layout.addWidget(QLabel("Set size (N): ", self))
self.N_slider_label = QLabel(self)
self.N_slider = QSlider(Qt.Horizontal, self)
self.N_slider.valueChanged.connect(self.handleNSliderChange)
self.N_slider_layout.addWidget(self.N_slider)
self.N_slider_layout.addWidget(self.N_slider_label)
# wether to refresh edges each time or keep edges to add to/remove from
self.refresh_edges_checkbox = QCheckBox(
"Refresh Edges instead of Adding/Removing", self)
self.refresh_edges_checkbox.stateChanged.connect(
self.handleRefreshCheckboxChange)
self.settingslayout.addWidget(self.refresh_edges_checkbox)
self.settingslayout.addSpacerItem(
QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding))
self.plot_widget = PlotWidget(name="clustersize by p")
self.settingslayout.addWidget(self.plot_widget)
self.plot_widget.setLabel('left', 'maximum cluster size', units='%')
self.plot_widget.setLabel('bottom', 'p', units='')
self.plot_widget.setXRange(0, 1)
self.plot_widget.setYRange(0, 1)
self.plot = ScatterPlotItem()
self.plot_widget.addItem(self.plot)
self.plot_clear_button = QPushButton("Clear plot")
self.plot_clear_button.clicked.connect(self.handlePlotClearButton)
self.settingslayout.addWidget(self.plot_clear_button)
self.settingswidget.setLayout(self.settingslayout)
self.settingswidget.setMinimumSize(50, 50)
self.splitter.addWidget(self.settingswidget)
self.splitter.addWidget(self.percolationWidget)
self.layout.addWidget(self.splitter)
self.percolationWidget.graphUpdated.connect(self.handleGraphUpdated)
self.setWindowTitle('Percolation Model')
self.setFocus()
class AttributeViewer(QWidget):
"""
Show a scatter plot of two attributes from a set of localizations.
init
----
locs_path : str, path to a CSV with localization
data
max_spots : int, the maximum number of spots to
plot. It's often too costly to render
more than 30000 spots or so
gui_size : int
parent : root QWidget
"""
def __init__(self, locs_path, max_spots=10000, gui_size=600, parent=None):
super(AttributeViewer, self).__init__(parent=parent)
self.locs_path = locs_path
self.max_spots = max_spots
self.gui_size = gui_size
self.initData()
self.initUI()
def initData(self):
"""
Load the spots data.
"""
# Load the locs dataframe
self.locs = pd.read_csv(self.locs_path).sort_values(by='frame')
# If too many spots, truncate the dataframe
if len(self.locs) > self.max_spots:
print("Truncating dataframe to %d spots" % self.max_spots)
self.locs = self.locs[:self.max_spots]
else:
print("Plotting %d spots" % len(self.locs))
# List of available attributes to display
dtypes = [
'float64', 'float', 'int64', 'int32', 'uint16', 'uint8', 'int'
]
self.parameters = [c for c in self.locs.columns if \
self.locs[c].dtype in dtypes]
# Generate colormap
self.n_colors = 1000
self.cmap = cm.get_cmap('viridis', self.n_colors)
self.cmap_hex = np.array([mpl_colors.rgb2hex(self.cmap(i)[:3]) \
for i in range(self.n_colors)])
def initUI(self):
"""
Initialize the user interface.
"""
# Main window
self.win = QWidget()
L = QGridLayout(self.win)
self.win.resize(self.gui_size * 1.8, self.gui_size)
# Two subwindows: one on the left for the scatter plot
# and one on the right for widgets
self.win_left = QWidget(self.win)
self.win_right = QWidget(self.win)
L.addWidget(self.win_left, 0, 0, 1, 3)
L.addWidget(self.win_right, 0, 3, 1, 1)
L_left = QGridLayout(self.win_left)
L_right = QGridLayout(self.win_right)
# GraphicsLayoutWidget, to organize scatter plot and
# associated items
self.graphicsLayoutWidget = GraphicsLayoutWidget(parent=self.win_left)
# PlotItem, to contain the ScatterPlotItem
self.plotItem = self.graphicsLayoutWidget.addPlot()
L_left.addWidget(self.graphicsLayoutWidget, 0, 0)
# ScatterPlotItem, core data display
self.scatterPlotItem = ScatterPlotItem(symbol='o',
brush=None,
pxMode=True,
pen={
'color': '#FFFFFF',
'width': 4.0
},
size=4.0)
self.plotItem.addItem(self.scatterPlotItem)
## WIDGETS
widget_align = Qt.AlignTop
# Select parameter to map to the x-axis
self.M_par_0 = LabeledQComboBox(self.parameters,
"x-parameter",
init_value="x",
parent=self.win_right)
L_right.addWidget(self.M_par_0, 0, 0, alignment=widget_align)
self.M_par_0.assign_callback(self.M_par_callback)
# Select parameter to map to the y-axis
self.M_par_1 = LabeledQComboBox(self.parameters,
"y-parameter",
init_value="y",
parent=self.win_right)
L_right.addWidget(self.M_par_1, 1, 0, alignment=widget_align)
self.M_par_1.assign_callback(self.M_par_callback)
# Select which attribute to color the localizations by
options = self.parameters + ["density"]
self.M_color_by = LabeledQComboBox(options,
"Color by",
init_value="density",
parent=self.win_right)
L_right.addWidget(self.M_color_by, 0, 1, alignment=widget_align)
self.M_color_by.assign_callback(self.M_color_by_callback)
# Select the size of the window to use when computing
# localization density
window_size_options = [
str(j)
for j in [3, 5, 7, 9, 11, 13, 15, 19, 23, 31, 41, 61, 81, 101]
]
self.M_density_window = LabeledQComboBox(window_size_options,
"Density window",
init_value="7",
parent=self.win_right)
L_right.addWidget(self.M_density_window, 1, 1, alignment=widget_align)
self.M_density_window.assign_callback(self.M_density_window_callback)
# Button to induce a simpler representation that can handle
# more spots
self.simple_mode = False
self.B_simple = QPushButton("Simple scatter", parent=self.win_right)
L_right.addWidget(self.B_simple, 2, 0, alignment=widget_align)
self.B_simple.clicked.connect(self.B_simple_callback)
# Button to toggle log color scaling
self.log_scale_mode = True
self.B_log = QPushButton("Log color scale", parent=self.win_right)
self.B_log.clicked.connect(self.B_log_callback)
L_right.addWidget(self.B_log, 2, 1, alignment=widget_align)
# Empty widgets to manipulate the layout
n_rows = 15
for j in range(3, n_rows):
q = QWidget(self.win_right)
L_right.addWidget(q, j, 0)
# Show the main window
self.update_scatter()
self.win.show()
## CORE FUNCTIONS
def get_pars(self):
"""
Get the current attributes mapped to the x and y axes
of the scatter plot.
returns
-------
(str: x attribute, str: y attribute)
"""
return self.M_par_0.currentText(), self.M_par_1.currentText()
def update_scatter(self, rescale=True):
"""
Update the scatter plot.
args
----
rescale : change axis limits
"""
cx, cy = self.get_pars()
# In the special case of plotting x vs y, make sure
# that the aspect ratio is right
if ((cx == 'x') and (cy == 'y')) or ((cx == 'y') and (cy == 'x')):
self.plotItem.setAspectLocked(lock=True)
else:
self.plotItem.setAspectLocked(lock=False)
# Update the scatter plots
if self.simple_mode:
self.scatter_simple(cx, cy)
else:
self.scatter_color(cx, cy)
# Set axis labels
labelStyle = {'font-size': '18pt'}
self.plotItem.setLabel('bottom', text=cx, **labelStyle)
self.plotItem.setLabel('left', text=cy, **labelStyle)
# Change axis limits
if rescale:
self.plotItem.autoBtnClicked()
def scatter_color(self, cx, cy):
"""
Load the current set of data into a new scatter plot,
coloring by the current "color by" attribute.
args
----
cx, cy : str, columns in self.locs
"""
self.scatterPlotItem.setData(size=4.0, brush=None)
color_attrib = self.M_color_by.currentText()
if color_attrib == 'density':
densities, spots = self.make_density(cx, cy)
else:
spots = self.make_attrib_colors(color_attrib)
self.scatterPlotItem.setData(spots=spots)
def scatter_simple(self, cx, cy):
"""
A simpler way of representing the data, using black
and white only.
args
----
cx, cy : str, columns in self.locs
"""
self.scatterPlotItem.setData(self.locs[cx],
self.locs[cy],
pen=pg.mkPen(None),
brush=pg.mkBrush(255, 255, 255, 10),
size=10)
def make_density(self, c0, c1):
"""
Get the normalized density of points along the (c0, c1)
axis in the set of localizations.
args
----
c0, c1 : str, columns in self.locs
returns
-------
(
1D ndarray, the density of each point;
dict, argument to pass to ScatterPlotItem.setData
)
"""
# Get the current density window size
w = int(self.M_density_window.currentText())
# Format the desired two attributes as ndarray for
# fast indexing
data = np.asarray(self.locs[[c0, c1]])
# Each of the attributes could have very different
# magnitudes, so scale the distances relative to the
# difference between the 5th and 95th percentiles for
# each attribute.
# Special case: x and y get the same scaling
if ((c0 == 'x') and (c1 == 'y')) or ((c0 == 'y') and (c1 == 'x')):
ybinsize = 1.0
xbinsize = 1.0
else:
norm = 400.0
ybinsize = (np.percentile(self.locs[c0], 95) - \
np.percentile(self.locs[c0], 5)) / norm
xbinsize = (np.percentile(self.locs[c1], 95) - \
np.percentile(self.locs[c1], 5)) / norm
# Create the binning scheme from these bin sizes
ybinedges = np.arange(np.percentile(self.locs[c0], 0.1),
np.percentile(self.locs[c0], 99.9), ybinsize)
xbinedges = np.arange(np.percentile(self.locs[c1], 0.1),
np.percentile(self.locs[c1], 99.9), xbinsize)
# Bin the data
H, _yedges, _xedges = np.histogram2d(self.locs[c0],
self.locs[c1],
bins=(ybinedges, xbinedges))
# Count the number of points in the neighborhood
# of each point
density = uniform_filter(H, w)
# Digitize the data according to the binning scheme
# X_int = ((data - np.array([ybinedges.min(), xbinedges.min()])) / \
# np.array([ybinsize, xbinsize])).astype('int64')
# data_y_int = X_int[:,0]
# data_x_int = X_int[:,1]
data_y_int = np.digitize(data[:, 0], ybinedges)
data_x_int = np.digitize(data[:, 1], xbinedges)
# Determine which data points fall within the binning
# scheme
inside = (data_y_int>=0) & (data_x_int>=0) & \
(data_y_int<(len(ybinedges)-1)) & \
(data_x_int<(len(xbinedges)-1))
data_y_int_inside = data_y_int[inside]
data_x_int_inside = data_x_int[inside]
# Retrieve the densities for each point
point_densities = np.empty(data.shape[0], dtype=density.dtype)
point_densities[inside] = density[data_y_int_inside, data_x_int_inside]
# Set points outside the binning scheme to density 1
point_densities[~inside] = 1.0
# Rescale a little
point_densities = point_densities * (w**2)
point_densities[point_densities <= 0] = 0.001
# Log-scale
if self.log_scale_mode:
point_densities = np.log(point_densities) / np.log(2.0)
point_densities[point_densities < 0.0] = 0.0
# Rescale the point densities into color indices
R = (point_densities * (self.n_colors - 1) /
point_densities.max()).astype(np.int64)
R[~inside] = 0
spot_colors = self.cmap_hex[R]
# Format the plotting spot dict
spots = [{'pos': data[i,:], 'pen': {'color': spot_colors[i], 'width': 3.0}} \
for i in range(data.shape[0])]
return point_densities, spots
def make_attrib_colors(self, attrib):
"""
Generate a spot format in which the color of each spot
is keyed to a particular attribute, with appropriate
rescaling for the different magnitudes of each attribute.
args
----
attrib : str, a column in self.locs
returns
-------
dict, parameters to pass to ScatterPlotItem.setData
"""
# Current axis attributes
c0, c1 = self.get_pars()
# Sort by ascending attribute
self.locs = self.locs.sort_values(by=attrib)
XY = np.asarray(self.locs[[c0, c1]])
Z = np.asarray(self.locs[attrib])
# Filter out unsanitary values
sanitary = (~np.isnan(Z)) & (~np.isinf(Z))
if (~sanitary).any():
print("Filtering out unsanitary values in %s" % attrib)
XY = XY[sanitary, :]
Z = Z[sanitary]
# Log scale
if self.log_scale_mode:
Z[Z <= 0.0] = 0.001
Z = np.log(Z) / np.log(2.0)
# Bin localizations by their relative value in
# the color attribute
norm = 400.0
try:
binsize = (np.percentile(Z, 95) - np.percentile(Z, 5)) / norm
binedges = np.arange(np.percentile(Z, 0.01),
np.percentile(Z, 99.9), binsize)
Z[Z < binedges.min()] = binedges.min()
Z[Z >= binedges.max()] = binedges.max() - binsize
assignments = np.digitize(Z, bins=binedges).astype('float64')
except ValueError:
print("Can't generate a color scale for %s; " \
"try turning off log scale" % attrib)
return []
# Scale into the available color indices
spot_colors = self.cmap_hex[((assignments * (self.n_colors-1)) / \
assignments.max()).astype(np.int64)]
# Generate the argument to ScatterPlotItem.setData
spots = [{'pos': XY[i,:], 'pen': {'color': spot_colors[i], 'width': 3.0}} \
for i in range(XY.shape[0])]
return spots
## WIDGET CALLBACKS
def M_par_callback(self):
"""
Change the attribute mapped to the axes.
"""
self.update_scatter(rescale=True)
def M_color_by_callback(self):
"""
Change which attribute is used to generate the color
scheme for the localizations.
"""
self.update_scatter(rescale=False)
def M_density_window_callback(self):
"""
Change the size of the window used to determine the local
density of each localization in the current plane.
"""
if self.M_color_by.currentText() == "density":
self.update_scatter(rescale=False)
def B_simple_callback(self):
"""
Change into simple plotting mode, which uses less memory
to render the plot but doesn't support color.
"""
self.simple_mode = not self.simple_mode
self.update_scatter(rescale=False)
def B_log_callback(self):
"""
Toggle between log and linear scales for the color map.
"""
self.log_scale_mode = not self.log_scale_mode
print("Log scale: ", self.log_scale_mode)
self.update_scatter(rescale=False)
def handlePlotClearButton(self):
self.plot = ScatterPlotItem()
self.plot_widget.clear()
self.plot_widget.addItem(self.plot)
self.plot_widget.update()
class DataInspectorLine(InfiniteLine):
"""
DataInspectorLine provides a moveable vertical line item that shows labels
containing the coordinates of the points of existing curves it touches.
It provides a method to attach it to a PlotItem.
.. todo:: for now it only works on the main viewbox.
"""
# TODO: support more than 1 viewbox (e.g. y2axis).
# TODO: modify anchor of labels so that they are plotted on the left if
# they do not fit in the view
def __init__(
self,
date_format="%Y-%m-%d %H:%M:%S",
y_format="%0.4f",
trigger_point_size=10,
):
super(DataInspectorLine, self).__init__(angle=90, movable=True)
self._labels = []
self._plot_item = None
self.y_format = y_format
self.trigger_point_size = trigger_point_size
self.date_format = date_format
self._label_style = "background-color: #35393C;"
self.sigPositionChanged.connect(self._inspect)
self._highlights = ScatterPlotItem(
pos=(),
symbol="s",
brush="35393C88",
pxMode=True,
size=trigger_point_size,
)
# hack to make the CurvesPropertiesTool ignore the highlight points
self._highlights._UImodifiable = False
def _inspect(self):
"""
Slot to re inspector line movemethe mouse move event, and perform
the action on the plot.
:param evt: mouse event
"""
xpos = self.pos().x()
x_px_size, _ = self.getViewBox().viewPixelSize()
self._removeLabels()
points = []
# iterate over the existing curves
for c in self._plot_item.curves:
if c is self._highlights:
continue
if c.xData is not None:
# find the index of the closest point of this curve
adiff = numpy.abs(c.xData - xpos)
idx = numpy.argmin(adiff)
# only add a label if the line touches the symbol
tolerance = 0.5 * max(1, c.opts["symbolSize"]) * x_px_size
if adiff[idx] < tolerance:
points.append((c.xData[idx], c.yData[idx]))
self._createLabels(points)
def _createLabels(self, points):
for x, y in points:
# create label at x,y
_x = self._getXValue(x)
_y = self._getYValue(y)
text_item = TextItem()
text_item.setPos(x, y)
text_item.setHtml(("<div style='{}'> " + "<span><b>x=</b>{} " +
"<span><b>y=</b>{}</span> " + "</div>").format(
self._label_style, _x, _y))
self._labels.append(text_item)
self._plot_item.addItem(text_item, ignoreBounds=True)
# Add "highlight" marker at each point
self._highlights.setData(pos=points)
def _getXValue(self, x):
"""
Helper method converting x value to time if necessary
:param x: current x value
:return: time or normal x value (depends of the x axis type)
"""
x_axis = self._plot_item.getAxis("bottom")
if isinstance(x_axis, DateAxisItem):
return self._timestampToDateTime(x)
else:
return x
def _getYValue(self, y):
return str(self.y_format % y)
def _timestampToDateTime(self, timestamp):
"""
Method used to caste the timestamp from the curve to date
in proper format (%Y-%m-%d %H:%M:%S)
:param timestamp: selected timestamp from curve
"""
return datetime.utcfromtimestamp(timestamp).strftime(self.date_format)
def _removeLabels(self):
# remove existing texts
for item in self._labels:
self.getViewBox().removeItem(item)
self._labels = []
# remove existing highlights
self._highlights.setData(pos=())
def attachToPlotItem(self, plot_item):
"""
Method to attach :class:`DataInspectorLine` to the plot
:param plot: to attach
"""
self._plot_item = plot_item
self._plot_item.addItem(self, ignoreBounds=True)
self._plot_item.addItem(self._highlights, ignoreBounds=True)
def dettach(self):
"""
Method use to detach the class:`DataInspectorLine` from the plot
"""
self._removeLabels()
self._plot_item.removeItem(self._highlights)
self._plot_item.removeItem(self)
self._plot_item = None
class CentroidScatterPlotWidget(QWidget, Ui_ScatterPlot):
"""This class handles managing the centroid scatter plot and the histogram
projections for both x and y coordinates.
Attributes
----------
brushColor : tuple
The common color for all brushes in the widget.
brushes : list
A set of brushes with varying alpha.
dataCounter : int
Number of times data arrays have been appended to up until array size.
dataSize : int
The requested size of the data arrays.
histogramFillBrush : QtGui.QBrush
Brush used to fill the projection histograms.
maxAlpha : int
The maximum transparency value for a brush
minAlpha : int
The minimum transparency value for a brush.
numBins : int
Number of histogram bins for the projections.
penColor : tuple
The outline color for all the points.
pointBrush : QtGui.QBrush
The brush for the scatter plot points.
pointPen : QtGui.QPen
The outline pen for the scatter plot points.
rollArray : bool
Flag as to when to start rolling the data arrays of centroid values.
scatterPlotItem : pyqtgraph.ScatterPlotItem
Instance of the centroid scatter plot.
xData : numpy.array
Container for the x coordinate of the centroid.
xHistogramItem : pyqtgraph.PlotItem
Instance of the x coordinate histogram projection.
yData : numpy.array
Container for the y coordinate of the centroid.
yHistogramItem : pyqtgraph.PlotItem
Instance of the y coordinate histogram projection.
"""
def __init__(self, parent=None):
"""Initialize the class.
Parameters
----------
parent : None, optional
Top-level widget.
"""
super().__init__(parent)
self.setupUi(self)
p1 = self.scatterPlot.addPlot()
self.scatterPlotItem = ScatterPlotItem()
p1.addItem(self.scatterPlotItem)
p1.setLabel('left', 'Y', units='pixel')
p1.setLabel('bottom', 'X', units='pixel')
self.yHistogramItem = None
self.xHistogramItem = None
self.numBins = 40
self.dataSize = None
self.xData = None
self.yData = None
self.rollArray = False
self.dataCounter = 0
self.brushes = None
self.brushColor = (159, 159, 159)
self.penColor = (255, 255, 255)
self.maxAlpha = 255
self.minAlpha = 127
self.histogramFillBrush = mkBrush(*self.brushColor, 200)
self.pointBrush = mkBrush(*self.brushColor, self.maxAlpha)
self.pointPen = mkPen(*self.penColor)
self.scatterPlotItem.setBrush(self.pointBrush)
def clearPlot(self):
"""Reset all data and clear the plot.
"""
self.rollArray = False
self.dataCounter = 0
self.xData = np.array([])
self.yData = np.array([])
self.scatterPlotItem.setData(self.xData, self.yData)
self.xHistogramItem.setData([], [], stepMode=False)
self.yHistogramItem.setData([], [], stepMode=False)
self.scatterPlotItem.getViewBox().setRange(xRange=(0, 1),
yRange=(0, 1),
disableAutoRange=False)
self.xHistogramItem.getViewBox().setRange(xRange=(0, 1),
yRange=(0, 1),
disableAutoRange=False)
self.yHistogramItem.getViewBox().setRange(xRange=(0, 1),
yRange=(0, 1),
disableAutoRange=False)
def getConfiguration(self):
"""Get the current plot configuration.
Returns
-------
int
The set of current configuration parameters.
"""
return self.numBins
def makeBrushes(self):
"""Make brushes for spots with differnet alpha factors.
"""
self.brushes = []
deltaAlpha = self.maxAlpha - self.minAlpha
slope = deltaAlpha / (self.dataSize - 1)
for i in range(self.dataSize):
alpha = slope * i + self.minAlpha
self.brushes.append(mkBrush(*self.brushColor, int(alpha)))
#c = int(alpha)
#self.brushes.append(mkBrush(c, c, c, self.maxAlpha))
def setArraySize(self, arraySize):
"""Update the stored array size and adjust arrays.
Parameters
----------
arraySize : int
The new array size to use.
"""
self.dataSize = arraySize
self.xData = np.array([])
self.yData = np.array([])
self.makeBrushes()
self.rollArray = False
def setConfiguration(self, config):
"""Set the new parameters into the widget.
Parameters
----------
config : `config.CentroidPlotConfig`
The new parameters to apply.
"""
self.numBins = config.numHistogramBins
def setup(self, arraySize):
"""Provide information for setting up the plot.
Parameters
----------
arraySize : int
The size for the plot data arrays.
"""
self.dataSize = arraySize
self.xData = np.array([])
self.yData = np.array([])
self.makeBrushes()
p1 = self.yHistogram.addPlot()
self.yHistogramItem = p1.plot(self.yData, self.yData)
self.yHistogramItem.setRotation(90)
p2 = self.xHistogram.addPlot()
self.xHistogramItem = p2.plot(self.xData, self.xData)
def updateData(self, centroidX, centroidY):
"""Update the data arrays with a new centroid coordinate pair.
Parameters
----------
centroidX : float
The current x coordinate of the centroid to plot.
centroidY : float
The current y coordinate of the centroid to plot.
"""
if self.rollArray:
self.xData[:-1] = self.xData[1:]
self.xData[-1] = centroidX
self.yData[:-1] = self.yData[1:]
self.yData[-1] = centroidY
else:
# This does create copies of arrays, so watch performance.
self.xData = np.append(self.xData, centroidX)
self.yData = np.append(self.yData, centroidY)
if self.dataCounter < self.dataSize:
self.dataCounter += 1
if self.dataCounter == self.dataSize:
self.rollArray = True
def showPlot(self):
"""Show the scatter and histogram plots.
"""
self.scatterPlotItem.setData(self.xData,
self.yData,
pen=self.pointPen,
brush=self.brushes)
xy, xx = np.histogram(self.xData,
bins=np.linspace(np.min(self.xData),
np.max(self.xData),
self.numBins))
self.xHistogramItem.setData(xx,
xy,
stepMode=True,
fillLevel=0,
fillBrush=self.histogramFillBrush)
yy, yx = np.histogram(self.yData,
bins=np.linspace(np.min(self.yData),
np.max(self.yData),
self.numBins))
# Flip due to rotated plot
yy *= -1
self.yHistogramItem.setData(yx,
yy,
stepMode=True,
fillLevel=0,
fillBrush=self.histogramFillBrush)
class AppWidget(QWidget):
def __init__(self):
QWidget.__init__(self)
self.graph_types = [Lattice_2d, Triangles_2d, Honeycomb_2d, Lattice_3d]
self.graph_names = [
"2D-Grid", "2D-Triangles", "2D-Honeycomb", "3D-Grid"
]
self.setupLayout()
self.setSettings()
def setSettings(self):
self.graph_type_combobox.setCurrentIndex(0)
self.p_slider.setValue(100)
self.N_slider.setValue(5)
self.refresh_edges_checkbox.setCheckState(Qt.Checked)
def setupLayout(self):
self.layout = QHBoxLayout(self)
self.splitter = QSplitter(Qt.Horizontal)
self.settingswidget = QWidget(self)
self.settingswidget.setMaximumWidth(400)
self.settingslayout = QVBoxLayout()
self.percolationWidget = PercolationWidget()
self.graph_type_combobox = QComboBox(self)
self.graph_type_combobox.addItems(self.graph_names)
self.graph_type_combobox.currentIndexChanged.connect(
self.handleGraphTypeChanged)
self.graph_type_combobox.setFocusPolicy(Qt.NoFocus)
self.settingslayout.addWidget(self.graph_type_combobox)
self.p_slider_layout = QHBoxLayout()
self.settingslayout.addLayout(self.p_slider_layout)
self.p_slider_layout.addWidget(QLabel("Set p value: ", self))
self.p_slider_label = QLabel(self)
self.p_slider = QSlider(Qt.Horizontal, self)
self.p_slider.valueChanged.connect(self.handlePSliderChange)
self.p_slider_layout.addWidget(self.p_slider)
self.p_slider_layout.addWidget(self.p_slider_label)
self.N_slider_layout = QHBoxLayout()
self.settingslayout.addLayout(self.N_slider_layout)
self.N_slider_layout.addWidget(QLabel("Set size (N): ", self))
self.N_slider_label = QLabel(self)
self.N_slider = QSlider(Qt.Horizontal, self)
self.N_slider.valueChanged.connect(self.handleNSliderChange)
self.N_slider_layout.addWidget(self.N_slider)
self.N_slider_layout.addWidget(self.N_slider_label)
# wether to refresh edges each time or keep edges to add to/remove from
self.refresh_edges_checkbox = QCheckBox(
"Refresh Edges instead of Adding/Removing", self)
self.refresh_edges_checkbox.stateChanged.connect(
self.handleRefreshCheckboxChange)
self.settingslayout.addWidget(self.refresh_edges_checkbox)
self.settingslayout.addSpacerItem(
QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding))
self.plot_widget = PlotWidget(name="clustersize by p")
self.settingslayout.addWidget(self.plot_widget)
self.plot_widget.setLabel('left', 'maximum cluster size', units='%')
self.plot_widget.setLabel('bottom', 'p', units='')
self.plot_widget.setXRange(0, 1)
self.plot_widget.setYRange(0, 1)
self.plot = ScatterPlotItem()
self.plot_widget.addItem(self.plot)
self.plot_clear_button = QPushButton("Clear plot")
self.plot_clear_button.clicked.connect(self.handlePlotClearButton)
self.settingslayout.addWidget(self.plot_clear_button)
self.settingswidget.setLayout(self.settingslayout)
self.settingswidget.setMinimumSize(50, 50)
self.splitter.addWidget(self.settingswidget)
self.splitter.addWidget(self.percolationWidget)
self.layout.addWidget(self.splitter)
self.percolationWidget.graphUpdated.connect(self.handleGraphUpdated)
self.setWindowTitle('Percolation Model')
self.setFocus()
def handleGraphTypeChanged(self, index):
if (self.graph_types[index].dim == 3):
self.N_slider.setValue(10)
self.graph = self.graph_types[index](self.N_slider.value())
self.percolationWidget.setGraph(self.graph)
self.setFocus()
def handlePSliderChange(self, value):
self.percolationWidget.setPValue(value)
self.p_slider_label.setText(str(value) + " %")
def handleNSliderChange(self, value):
self.graph = self.graph_types[self.graph_type_combobox.currentIndex()](
value)
self.percolationWidget.setGraph(self.graph)
self.N_slider_label.setText(str(value))
def handleRefreshCheckboxChange(self, value):
self.percolationWidget.setRefresh(value == Qt.Checked)
def handleGraphUpdated(self, p, clustersize):
self.plot.addPoints(x=[p], y=[clustersize])
def handlePlotClearButton(self):
self.plot = ScatterPlotItem()
self.plot_widget.clear()
self.plot_widget.addItem(self.plot)
self.plot_widget.update()
def keyPressEvent(self, event):
if event.key() in [
Qt.Key_W, Qt.Key_A, Qt.Key_S, Qt.Key_D, Qt.Key_Q, Qt.Key_E,
Qt.Key_Plus, Qt.Key_Minus
]:
self.percolationWidget.graphwidget.keyPressEvent(event)
elif event.key() == Qt.Key_Tab:
self.setFocus()
else:
QWidget.keyPressEvent(self, event)
def initUI(self):
"""
Initialize the user interface.
"""
# Main window
self.win = QWidget()
L = QGridLayout(self.win)
self.win.resize(self.gui_size * 1.8, self.gui_size)
# Two subwindows: one on the left for the scatter plot
# and one on the right for widgets
self.win_left = QWidget(self.win)
self.win_right = QWidget(self.win)
L.addWidget(self.win_left, 0, 0, 1, 3)
L.addWidget(self.win_right, 0, 3, 1, 1)
L_left = QGridLayout(self.win_left)
L_right = QGridLayout(self.win_right)
# GraphicsLayoutWidget, to organize scatter plot and
# associated items
self.graphicsLayoutWidget = GraphicsLayoutWidget(parent=self.win_left)
# PlotItem, to contain the ScatterPlotItem
self.plotItem = self.graphicsLayoutWidget.addPlot()
L_left.addWidget(self.graphicsLayoutWidget, 0, 0)
# ScatterPlotItem, core data display
self.scatterPlotItem = ScatterPlotItem(symbol='o',
brush=None,
pxMode=True,
pen={
'color': '#FFFFFF',
'width': 4.0
},
size=4.0)
self.plotItem.addItem(self.scatterPlotItem)
## WIDGETS
widget_align = Qt.AlignTop
# Select parameter to map to the x-axis
self.M_par_0 = LabeledQComboBox(self.parameters,
"x-parameter",
init_value="x",
parent=self.win_right)
L_right.addWidget(self.M_par_0, 0, 0, alignment=widget_align)
self.M_par_0.assign_callback(self.M_par_callback)
# Select parameter to map to the y-axis
self.M_par_1 = LabeledQComboBox(self.parameters,
"y-parameter",
init_value="y",
parent=self.win_right)
L_right.addWidget(self.M_par_1, 1, 0, alignment=widget_align)
self.M_par_1.assign_callback(self.M_par_callback)
# Select which attribute to color the localizations by
options = self.parameters + ["density"]
self.M_color_by = LabeledQComboBox(options,
"Color by",
init_value="density",
parent=self.win_right)
L_right.addWidget(self.M_color_by, 0, 1, alignment=widget_align)
self.M_color_by.assign_callback(self.M_color_by_callback)
# Select the size of the window to use when computing
# localization density
window_size_options = [
str(j)
for j in [3, 5, 7, 9, 11, 13, 15, 19, 23, 31, 41, 61, 81, 101]
]
self.M_density_window = LabeledQComboBox(window_size_options,
"Density window",
init_value="7",
parent=self.win_right)
L_right.addWidget(self.M_density_window, 1, 1, alignment=widget_align)
self.M_density_window.assign_callback(self.M_density_window_callback)
# Button to induce a simpler representation that can handle
# more spots
self.simple_mode = False
self.B_simple = QPushButton("Simple scatter", parent=self.win_right)
L_right.addWidget(self.B_simple, 2, 0, alignment=widget_align)
self.B_simple.clicked.connect(self.B_simple_callback)
# Button to toggle log color scaling
self.log_scale_mode = True
self.B_log = QPushButton("Log color scale", parent=self.win_right)
self.B_log.clicked.connect(self.B_log_callback)
L_right.addWidget(self.B_log, 2, 1, alignment=widget_align)
# Empty widgets to manipulate the layout
n_rows = 15
for j in range(3, n_rows):
q = QWidget(self.win_right)
L_right.addWidget(q, j, 0)
# Show the main window
self.update_scatter()
self.win.show()
def __init__(self, manager: BarManager):
""""""
ScatterPlotItem.__init__(self)
super(CandleItem,self).__init__(manager)
self.orders : Dict[int,Dict[str,OrderData]] = {} # {ix:{orderid:order}}
class CrystfelImage(QObject):
def __init__(self, imodel, iview, geom, parent=None):
QObject.__init__(self, parent)
self.imodel = imodel
self.dmodel = imodel.model
self.iview = iview
self.iview.ui.menuBtn.hide()
self.iview.ui.roiBtn.hide()
# Thanks CXIVIEW, Anton & Valerio
pos = np.array([0.0, 0.5, 1.0])
color = np.array(
[[255, 255, 255, 255], [128, 128, 128, 255], [0, 0, 0, 255]],
dtype=np.ubyte)
new_color_map = ColorMap(pos, color)
self.iview.ui.histogram.gradient.setColorMap(new_color_map)
self.lastrow = -1
self.curFileName = None
self.curFile = None
self.canDraw = self.dmodel.canSaveLst()
self.checkEvent = "event" in self.dmodel.cols
self.yxmap = None
self.slab_shape = None
self.img_shape = None
self.geom_coffset = 0
self.geom_pixsize = None
self.im_out = None
self.resolutionLambda = None
self.pixRadiusToRes = None
self.hkl = None
self.hklLookup = None
self.imodel.dataChanged.connect(self.draw)
self.iview.view.menu.addSeparator()
openGeomAct = self.iview.view.menu.addAction("Load CrystFEL Geometry")
openGeomAct.triggered.connect(self.openGeom)
peakmenu = self.iview.view.menu.addMenu("Peaks")
self.peakActionGroup = QActionGroup(self)
self.peakActionGroup.setExclusive(True)
self.peakActionGroup.triggered.connect(self.drawPeaks)
peakNone = peakmenu.addAction("None")
peakNone.setCheckable(True)
peakNone.setChecked(True)
peakNone.setData(0)
self.peakActionGroup.addAction(peakNone)
peakCXI = peakmenu.addAction("CXI")
peakCXI.setCheckable(True)
peakCXI.setEnabled(self.dmodel.canSaveLst())
peakCXI.setData(1)
self.peakActionGroup.addAction(peakCXI)
peakStream = peakmenu.addAction("Stream")
peakStream.setCheckable(True)
peakStream.setEnabled(self.dmodel.hasStreamPeaks())
peakStream.setData(2)
self.peakActionGroup.addAction(peakStream)
self.peakCanvas = ScatterPlotItem()
self.iview.getView().addItem(self.peakCanvas)
reflectionmenu = self.iview.view.menu.addMenu("Reflections")
self.reflectionActionGroup = QActionGroup(self)
self.reflectionActionGroup.setExclusive(True)
self.reflectionActionGroup.triggered.connect(self.drawReflections)
refNone = reflectionmenu.addAction("None")
refNone.setCheckable(True)
refNone.setChecked(True)
refNone.setData(0)
self.reflectionActionGroup.addAction(refNone)
refStream = reflectionmenu.addAction("Stream")
refStream.setCheckable(True)
refStream.setEnabled(self.dmodel.hasStreamReflections())
refStream.setData(1)
self.reflectionActionGroup.addAction(refStream)
self.reflectionCanvas = ScatterPlotItem()
self.iview.getView().addItem(self.reflectionCanvas)
self.drawResRingsAct = self.iview.view.menu.addAction(
"Resolution Rings")
self.drawResRingsAct.setCheckable(True)
self.drawResRingsAct.setChecked(False)
self.drawResRingsAct.triggered.connect(self.drawResRings)
self.drawResRingsAct.setEnabled(self.yxmap is not None)
self.resolutionRingsCanvas = ScatterPlotItem()
self.iview.getView().addItem(self.resolutionRingsCanvas)
self.resRingsTextItems = []
for x in self.dmodel.cfg.viewerResolutionRingsAngstroms:
self.resRingsTextItems.append(TextItem('', anchor=(0.5, 0.8)))
self.iview.getView().addItem(self.resRingsTextItems[-1])
self.drawResolutionLimitAct = self.iview.view.menu.addAction(
"Resolution Limit Ring")
self.drawResolutionLimitAct.setCheckable(True)
self.drawResolutionLimitAct.setChecked(False)
self.drawResolutionLimitAct.triggered.connect(self.drawResLimitRing)
self.drawResolutionLimitAct.setEnabled(
self.yxmap is not None and 'reslim' in self.dmodel.cols)
self.resolutionLimitCanvas = ScatterPlotItem()
self.iview.getView().addItem(self.resolutionLimitCanvas)
if geom is not None:
self.loadGeom(geom)
self.toolTipsAct = self.iview.view.menu.addAction(
"Show Position in Tool Tip")
self.toolTipsAct.setCheckable(True)
self.toolTipsAct.setChecked(True)
self.iview.scene.sigMouseMoved.connect(self.mouseMove)
self.draw()
def draw(self):
if not self.canDraw or self.imodel.currow == self.lastrow:
return
# Load the image
image = self.image()
if image is None:
return # Problem with file, don't try to load anything else
# Image was loaded, so update what we've currently got drawn
self.lastrow = self.imodel.currow
# Apply geometry
if self.yxmap is None:
image = np.transpose(image)
else:
image = cfel_geom.apply_geometry_from_pixel_maps(
image, self.yxmap, self.im_out)
self.iview.setImage(image, autoLevels=False, autoRange=False)
# CXI View Scaling
bottom, top = histogram_clip_levels(
image.ravel(), self.dmodel.cfg.cxiviewHistClipLevelValue)
self.iview.setLevels(bottom, top)
self.iview.getHistogramWidget().setHistogramRange(
min(bottom, self.dmodel.cfg.cxiviewHistMin),
max(top, self.dmodel.cfg.cxiviewHistMax),
padding=self.dmodel.cfg.cxiviewHistPadding)
self.calcResLambda()
self.drawPeaks()
self.drawReflections()
self.drawResRings()
self.drawResLimitRing()
def loadGeom(self, filename):
self.yxmap, self.slab_shape, self.img_shape = cfel_geom.pixel_maps_for_image_view(
filename)
self.im_out = np.zeros(self.img_shape, dtype=np.dtype(float))
self.geom_coffset = cfel_geom.coffset_from_geometry_file(filename)
self.geom_pixsize = 1 / cfel_geom.res_from_geometry_file(filename)
self.drawResRingsAct.setEnabled(True)
self.drawResolutionLimitAct.setEnabled('reslim' in self.dmodel.cols)
self.lastrow = -1
self.draw()
def openGeom(self):
name = QFileDialog.getOpenFileName(
self.iview,
'Select CrystFEL Geomery File (.geom)',
filter='*.geom')
if qt5:
if name:
self.loadGeom(name[0])
elif name is not None and len(name):
self.loadGeom(name)
def mouseMove(self, pos):
mapped = self.iview.getView().mapSceneToView(pos)
txt = ""
if self.toolTipsAct.isChecked() and self.iview.image is not None \
and mapped.x() >= 0 and mapped.x() < self.iview.image.shape[0] \
and mapped.y() >= 0 and mapped.y() < self.iview.image.shape[1]:
if self.img_shape is not None:
x = mapped.x() - self.img_shape[0] / 2
y = self.img_shape[1] / 2 - mapped.y()
else:
x = mapped.x()
y = mapped.y()
txt = "x: %i, y: %i" % (x, y)
if self.iview.image is not None:
txt += " value: %.2f" % self.iview.image[int(mapped.x()),
int(mapped.y())]
if self.pixRadiusToRes is not None:
txt += " resolution: %.2f" % self.pixRadiusToRes(
np.sqrt(x**2 + y**2))
if self.hklLookup is not None:
res = self.hklLookup.query([mapped.x(), mapped.y()], k=1)
if len(res
) > 0 and res[0] < self.dmodel.cfg.viewerReflectionSize:
txt += " hkl: %s" % self.hkl[res[1]]
self.iview.setToolTip(txt)
# Sub functions called by draw, not meant to be called externally
def fromMaybeEvent(self, paths):
r = None
for path in paths:
if path in self.curFile:
if self.checkEvent:
e = self.dmodel.data["event"][self.imodel.currow]
if e == -1: # No event
r = self.curFile[path]
else:
r = self.curFile[path][e]
else: # No events
r = self.curFile[path]
break
return r
def image(self):
image = None
ifile = self.dmodel.value("ifile", self.imodel.currow, False)
if ifile != self.curFileName:
if self.curFile is not None:
self.curFile.close()
self.curFileName = ifile
self.curFile = h5py.File(ifile, 'r')
image = self.fromMaybeEvent(self.dmodel.cfg.imageH5paths)
return image
def cxipeaks(self):
# Since this function should ideally only be called internally from draw,
# after image has been successfully generated, assume we have correct and valid ifile.
px = self.fromMaybeEvent(self.dmodel.cfg.peakXH5paths)
if px is None:
px = []
py = []
else:
if len(px.shape) > 1:
# Data is two dimension, assume x is first column and y second
py = px[:, 1]
px = px[:, 0]
else:
py = self.fromMaybeEvent(self.dmodel.cfg.peakYH5paths)
if py is None:
px = []
py = []
return px, py
def drawPeaks(self):
px = []
py = []
if self.peakActionGroup.checkedAction().data() == 1: # H5 Peaks
px, py = self.cxipeaks()
elif self.peakActionGroup.checkedAction().data() == 2: # Stream peaks
px, py = self.dmodel.streamPeaks(self.imodel.currow)
if self.yxmap is not None and len(px):
px = np.array(px, dtype=np.dtype(int))
py = np.array(py, dtype=np.dtype(int))
slab = py * self.slab_shape[1] + px
px = self.yxmap[0][slab]
py = self.yxmap[1][slab]
self.peakCanvas.setData(px,py,symbol=self.dmodel.cfg.viewerPeakSymbol,\
size=self.dmodel.cfg.viewerPeakSize,pen=\
mkPen(self.dmodel.cfg.viewerPeakColor,width=self.dmodel.cfg.viewerPeakPenWidth),\
brush=(0,0,0,0),pxMode=False)
def drawReflections(self):
px = []
py = []
self.hkl = None
self.hklLookup = None
if self.reflectionActionGroup.checkedAction().data() == 1: # Stream
px, py, self.hkl = self.dmodel.streamReflections(
self.imodel.currow)
if self.yxmap is not None and len(px):
px = np.array(px, dtype=np.dtype(int))
py = np.array(py, dtype=np.dtype(int))
slab = py * self.slab_shape[1] + px
px = self.yxmap[0][slab]
py = self.yxmap[1][slab]
self.reflectionCanvas.setData(px,py,symbol=self.dmodel.cfg.viewerReflectionSymbol,\
size=self.dmodel.cfg.viewerReflectionSize,pen=\
mkPen(self.dmodel.cfg.viewerReflectionColor,width=self.dmodel.cfg.viewerReflectionPenWidth),\
brush=(0,0,0,0),pxMode=False)
if self.hkl is not None:
self.hklLookup = scipy.spatial.cKDTree(np.dstack((px, py))[0])
def calcResLambda(self):
self.resolutionLambda = None
photon_ev = None
if "phoen" in self.dmodel.cols:
photon_ev = self.dmodel.data["phoen"][self.imodel.currow]
if photon_ev is None or photon_ev <= 0:
photon_ev = self.fromMaybeEvent(
self.dmodel.cfg.viewerPhotonEvH5Paths)
clen = None
if "aclen" in self.dmodel.cols:
clen = self.dmodel.data["aclen"][
self.imodel.currow] # Value is corrected with coffset
if clen is None:
clen = self.fromMaybeEvent(
self.dmodel.cfg.viewerCameraLengthH5Paths)
if clen is not None: # Uncorrected, correct here
clen += self.geom_coffset
# Need valid photon energy, camera length, and geometry (yxmap)
if photon_ev is None or photon_ev <= 0 or clen is None or self.yxmap is None:
return # Not enough info
lmbd = scipy.constants.h * scipy.constants.c / (scipy.constants.e *
photon_ev)
self.resolutionLambda=lambda r : (2.0/self.geom_pixsize)*(clen)*np.tan(2.0*np.arcsin(lmbd / \
(2.0 * r *1e-10)))
self.pixRadiusToRes = lambda r: 1e10 * lmbd / (2.0 * np.sin(
0.5 * np.arctan(r * self.geom_pixsize / clen)))
def drawResRings(self):
if not self.drawResRingsAct.isChecked(
) or self.resolutionLambda is None:
self.resolutionRingsCanvas.setData([], [])
for ti in self.resRingsTextItems:
ti.setText('')
else:
ring_sizes = self.resolutionLambda(
np.array(self.dmodel.cfg.viewerResolutionRingsAngstroms))
self.resolutionRingsCanvas.setData([self.img_shape[0]/2]*len(ring_sizes), [self.img_shape[1]/2]*len(ring_sizes),symbol='o',\
size=ring_sizes,pen=mkPen(self.dmodel.cfg.viewerResRingColor, width=self.dmodel.cfg.viewerResRingWidth),\
brush=(0,0,0,0),pxMode=False)
for i, ti in enumerate(self.resRingsTextItems):
ti.setText("%.1f A" %
self.dmodel.cfg.viewerResolutionRingsAngstroms[i],
color=self.dmodel.cfg.viewerResRingColor)
ti.setPos(self.img_shape[0] / 2,
self.img_shape[1] / 2 + ring_sizes[i] / 2)
def drawResLimitRing(self):
if not self.drawResolutionLimitAct.isChecked(
) or self.resolutionLambda is None:
self.resolutionLimitCanvas.setData([], [])
else:
r = self.dmodel.data['reslim'][self.imodel.currow]
if r <= 0:
self.resolutionLimitCanvas.setData([], [])
else:
r = 10 / r
self.resolutionLimitCanvas.setData([self.img_shape[0]/2], [self.img_shape[1]/2],symbol='o',\
size=self.resolutionLambda(r),\
pen=mkPen(self.dmodel.cfg.viewerResLimitRingColor, width=self.dmodel.cfg.viewerResLimitRingWidth),\
brush=(0,0,0,0),pxMode=False)
def initUI(self):
"""
Initialize the user interface.
"""
# Main window
self.win = QWidget()
# Figure out the GUI size
self.AR = float(self.imageReader.width) / self.imageReader.height
self.win.resize(self.gui_size*1.5, self.gui_size)
L_main = QGridLayout(self.win)
# A subwindow on the left for widgets, and a subwindow
# on the right for the image
self.win_right = QWidget(self.win)
self.win_left = QWidget(self.win)
L_right = QGridLayout(self.win_right)
L_left = QGridLayout(self.win_left)
L_main.addWidget(self.win_right, 0, 1, 1, 3)
L_main.addWidget(self.win_left, 0, 0, 1, 1)
## IMAGES / OVERLAYS
# ImageView, for rendering image
self.imageView = ImageView(parent=self.win_right)
L_right.addWidget(self.imageView, 0, 0)
# ScatterPlotItem, for overlaying localizations
self.scatterPlotItem = ScatterPlotItem()
self.scatterPlotItem.setParentItem(self.imageView.imageItem)
# GraphItem, for overlaying trajectory histories when
# desired
self.graphItem = GraphItem()
self.graphItem.setParentItem(self.imageView.imageItem)
# # Make spots clickable
self.lastClicked = []
self.scatterPlotItem.sigClicked.connect(self.spot_clicked)
## WIDGETS
widget_align = Qt.AlignTop
# Frame slider
self.frame_slider = IntSlider(minimum=0, interval=1,
maximum=self.imageReader.n_frames-1, init_value=self.start_frame,
name='Frame', parent=self.win_left)
L_left.addWidget(self.frame_slider, 0, 0, rowSpan=2,
alignment=widget_align)
self.frame_slider.assign_callback(self.frame_slider_callback)
# Button to toggle spot overlays
self.B_overlay_state = True
self.B_overlay = QPushButton("Overlay spots", parent=self.win_left)
self.B_overlay.clicked.connect(self.B_overlay_callback)
L_left.addWidget(self.B_overlay, 1, 0, alignment=widget_align)
# Button to toggle trajectory trails
self.B_overlay_trails_state = False
self.B_overlay_trails = QPushButton("Overlay histories", parent=self.win_left)
self.B_overlay_trails.clicked.connect(self.B_overlay_trails_callback)
L_left.addWidget(self.B_overlay_trails, 1, 1, alignment=widget_align)
self.B_overlay_trails.stackUnder(self.B_overlay)
# Menu to select current overlay symbol
symbol_options = keys_to_str(symbol_sizes.keys())
self.M_symbol = LabeledQComboBox(symbol_options, "Overlay symbol",
init_value="o", parent=self.win_left)
self.M_symbol.assign_callback(self.M_symbol_callback)
L_left.addWidget(self.M_symbol, 2, 0, alignment=widget_align)
# Menu to select how the spots are colored
color_by_options = ["None", "Trajectory", "Quantitative attribute", "Boolean attribute"]
self.M_color_by = LabeledQComboBox(color_by_options,
"Color spots by", init_value="None", parent=self.win_left)
self.M_color_by.assign_callback(self.M_color_by_callback)
L_left.addWidget(self.M_color_by, 3, 0, alignment=widget_align)
# Create a new binary spot condition
self.B_create_condition = QPushButton("Create Boolean attribute",
parent=self.win_left)
self.B_create_condition.clicked.connect(self.B_create_condition_callback)
L_left.addWidget(self.B_create_condition, 4, 0, alignment=widget_align)
# Select the binary column that determines color when "condition"
# is selected as the color-by attribute
condition_options = [c for c in self.locs.columns if self.locs[c].dtype == 'bool']
self.M_condition = LabeledQComboBox(condition_options, "Boolean attribute",
init_value="None", parent=self.win_left)
L_left.addWidget(self.M_condition, 3, 1, alignment=widget_align)
self.M_condition.assign_callback(self.M_condition_callback)
# Compare spots in a separate window that shows a grid of spots
self.B_compare_spots = QPushButton("Compare spots", parent=self)
L_left.addWidget(self.B_compare_spots, 2, 1, alignment=widget_align)
self.B_compare_spots.clicked.connect(self.B_compare_spot_callback)
# Some placeholder widgets, for better formatting
for j in range(6, 18):
q = QLabel(parent=self.win_left)
L_left.addWidget(q, j, 0, alignment=widget_align)
## KEYBOARD SHORTCUTS - tab right/left through frames
self.left_shortcut = QShortcut(QKeySequence(QtGui_Qt.Key_Left), self.win)
self.right_shortcut = QShortcut(QKeySequence(QtGui_Qt.Key_Right), self.win)
self.left_shortcut.activated.connect(self.tab_prev_frame)
self.right_shortcut.activated.connect(self.tab_next_frame)
## DISPLAY
self.update_image(autoRange=True, autoLevels=True, autoHistogramRange=True)
self.overlay_spots()
if "trajectory" in self.locs.columns:
self.M_color_by.setCurrentText("Trajectory")
self.M_color_by_callback()
self.win.show()
def render(self, intent):
if not self.canvas_widget:
bases_names = getattr(intent, 'mixins', tuple()) or tuple()
bases = map(
lambda name: plugin_manager.type_mapping['PlotMixinPlugin'][
name], bases_names)
self.canvas_widget = type('PlotViewBlend',
(*bases, PlotIntentCanvasBlend), {})()
self.layout().addWidget(self.canvas_widget)
self.canvas_widget.plotItem.addLegend()
items = []
if isinstance(intent, (PlotIntent, ErrorBarIntent, ScatterIntent)):
x = intent.x
if intent.x is not None:
x = np.asarray(intent.x).squeeze()
ys = np.asarray(intent.y).squeeze()
if ys.ndim == 1:
ys = [ys]
multicurves = False
else:
multicurves = True
symbol = intent.kwargs.get("symbol", None)
for i in range(len(ys)):
name = intent.name
if multicurves:
name += f' {i + 1}'
if isinstance(intent, ScatterIntent):
item = ScatterPlotItem(x=x,
y=ys[i],
name=name,
symbol=symbol)
self.canvas_widget.plotItem.addItem(item)
elif isinstance(intent, (PlotIntent, ErrorBarIntent)):
item = self.canvas_widget.plot(x=x,
y=ys[i],
name=name,
symbol=symbol)
items.append(item)
# Use most recent intent's log mode for the canvas's log mode
x_log_mode = intent.kwargs.get(
"xLogMode",
self.canvas_widget.plotItem.getAxis("bottom").logMode)
y_log_mode = intent.kwargs.get(
"yLogMode",
self.canvas_widget.plotItem.getAxis("left").logMode)
self.canvas_widget.plotItem.setLogMode(x=x_log_mode, y=y_log_mode)
self.canvas_widget.setLabels(**intent.labels)
if isinstance(intent, ErrorBarIntent):
kwargs = intent.kwargs.copy()
for key, value in kwargs.items():
if isinstance(value, DataArray):
kwargs[key] = np.asanyarray(value).squeeze()
erroritem = ErrorBarItem(x=np.asarray(intent.x).squeeze(),
y=np.asarray(intent.y).squeeze(),
**kwargs)
self.canvas_widget.plotItem.addItem(erroritem)
items.append(erroritem)
elif isinstance(intent, BarIntent):
kwargs = intent.kwargs.copy()
for key, value in kwargs.items():
if isinstance(value, DataArray):
kwargs[key] = np.asanyarray(value).squeeze()
if intent.x is not None:
kwargs['x'] = intent.x
baritem = pg.BarGraphItem(**kwargs)
self.canvas_widget.plotItem.addItem(baritem)
items.append(baritem)
self.intent_to_items[intent] = items
self.colorize()
return items
def __init__(self, manager: BarManager, am: ArrayManager):
""""""
ScatterPlotItem.__init__(self)
super(ExChartItem, self).__init__(manager, am)
self.orders: Dict[int, Dict[str, Order]] = {} # {ix:{orderid:order}}
class SpotViewer(QWidget):
"""
Overlay localizations or trajectories onto a raw movie.
Useful for QC.
The user sees a single image window with the current
frame and some overlaid localizations.
Each localization is either colored identically or
according to a color scheme. Available color schemes are
- color each localization by its trajectory index
(same color for locs in the same trajectory)
- color each localization by one of its numerical
attributes (e.g. intensity, BG, H_det, etc.)
- color each localization one of two colors according
to its value for a boolean attribute.
SpotViewer provides the user a way to create new boolean
attributes by thresholding attributes, via the "Create
Boolean attribute" button.
args
----
image_path : str, path to image file (e.g.
*.nd2, *.tif, or *.tiff)
locs_path : str, path to CSV with localizations
gui_size : int
start_frame : int, the initial frame shown
parent : root QWidget
"""
def __init__(self, image_path, locs_path, gui_size=800,
start_frame=0, parent=None):
super(SpotViewer, self).__init__(parent=parent)
self.image_path = image_path
self.locs_path = locs_path
self.gui_size = gui_size
self.start_frame = start_frame
self.initData()
self.initUI()
def initData(self):
"""
Load the datasets for this SpotViewer instance.
"""
# Make sure the required paths exist
assert os.path.isfile(self.image_path)
assert os.path.isfile(self.locs_path)
assert os.path.splitext(self.image_path)[1] in \
['.nd2', '.tif', '.tiff'], \
"Image file must be one of (*.nd2 *.tif *.tiff)"
# Make an image file reader
self.imageReader = ImageReader(self.image_path)
# Load the set of localizations
self.locs = pd.read_csv(self.locs_path)
# Some additional options if these localizations are
# assigned a trajectory
if 'trajectory' in self.locs.columns:
# Assign the traj_len, if it doesn't already exist
self.locs = traj_length(self.locs)
# Keep an array of localizations as an ndarray, for
# fast indexing when overlaying trajectory histories
self.tracks = np.asarray(
self.locs.loc[
self.locs['traj_len']>1,
['frame', 'trajectory', 'y', 'x']
].sort_values(by=['trajectory', 'frame'])
)
# Adjust for off-by-1/2 plot pixel indexing
self.tracks[:,2:] = self.tracks[:,2:] + 0.5
# Generate the set of colors
self.generate_color_schemes()
# Assign condition colors (initially all negative)
self.assign_condition_colors('y')
# Load the first round of spots
self.load_image(self.start_frame)
# Assign each trajectory a color
self.assign_traj_colors()
# Assign self.locs_curr, the current set of spots
self.load_spots(self.start_frame)
def initUI(self):
"""
Initialize the user interface.
"""
# Main window
self.win = QWidget()
# Figure out the GUI size
self.AR = float(self.imageReader.width) / self.imageReader.height
self.win.resize(self.gui_size*1.5, self.gui_size)
L_main = QGridLayout(self.win)
# A subwindow on the left for widgets, and a subwindow
# on the right for the image
self.win_right = QWidget(self.win)
self.win_left = QWidget(self.win)
L_right = QGridLayout(self.win_right)
L_left = QGridLayout(self.win_left)
L_main.addWidget(self.win_right, 0, 1, 1, 3)
L_main.addWidget(self.win_left, 0, 0, 1, 1)
## IMAGES / OVERLAYS
# ImageView, for rendering image
self.imageView = ImageView(parent=self.win_right)
L_right.addWidget(self.imageView, 0, 0)
# ScatterPlotItem, for overlaying localizations
self.scatterPlotItem = ScatterPlotItem()
self.scatterPlotItem.setParentItem(self.imageView.imageItem)
# GraphItem, for overlaying trajectory histories when
# desired
self.graphItem = GraphItem()
self.graphItem.setParentItem(self.imageView.imageItem)
# # Make spots clickable
self.lastClicked = []
self.scatterPlotItem.sigClicked.connect(self.spot_clicked)
## WIDGETS
widget_align = Qt.AlignTop
# Frame slider
self.frame_slider = IntSlider(minimum=0, interval=1,
maximum=self.imageReader.n_frames-1, init_value=self.start_frame,
name='Frame', parent=self.win_left)
L_left.addWidget(self.frame_slider, 0, 0, rowSpan=2,
alignment=widget_align)
self.frame_slider.assign_callback(self.frame_slider_callback)
# Button to toggle spot overlays
self.B_overlay_state = True
self.B_overlay = QPushButton("Overlay spots", parent=self.win_left)
self.B_overlay.clicked.connect(self.B_overlay_callback)
L_left.addWidget(self.B_overlay, 1, 0, alignment=widget_align)
# Button to toggle trajectory trails
self.B_overlay_trails_state = False
self.B_overlay_trails = QPushButton("Overlay histories", parent=self.win_left)
self.B_overlay_trails.clicked.connect(self.B_overlay_trails_callback)
L_left.addWidget(self.B_overlay_trails, 1, 1, alignment=widget_align)
self.B_overlay_trails.stackUnder(self.B_overlay)
# Menu to select current overlay symbol
symbol_options = keys_to_str(symbol_sizes.keys())
self.M_symbol = LabeledQComboBox(symbol_options, "Overlay symbol",
init_value="o", parent=self.win_left)
self.M_symbol.assign_callback(self.M_symbol_callback)
L_left.addWidget(self.M_symbol, 2, 0, alignment=widget_align)
# Menu to select how the spots are colored
color_by_options = ["None", "Trajectory", "Quantitative attribute", "Boolean attribute"]
self.M_color_by = LabeledQComboBox(color_by_options,
"Color spots by", init_value="None", parent=self.win_left)
self.M_color_by.assign_callback(self.M_color_by_callback)
L_left.addWidget(self.M_color_by, 3, 0, alignment=widget_align)
# Create a new binary spot condition
self.B_create_condition = QPushButton("Create Boolean attribute",
parent=self.win_left)
self.B_create_condition.clicked.connect(self.B_create_condition_callback)
L_left.addWidget(self.B_create_condition, 4, 0, alignment=widget_align)
# Select the binary column that determines color when "condition"
# is selected as the color-by attribute
condition_options = [c for c in self.locs.columns if self.locs[c].dtype == 'bool']
self.M_condition = LabeledQComboBox(condition_options, "Boolean attribute",
init_value="None", parent=self.win_left)
L_left.addWidget(self.M_condition, 3, 1, alignment=widget_align)
self.M_condition.assign_callback(self.M_condition_callback)
# Compare spots in a separate window that shows a grid of spots
self.B_compare_spots = QPushButton("Compare spots", parent=self)
L_left.addWidget(self.B_compare_spots, 2, 1, alignment=widget_align)
self.B_compare_spots.clicked.connect(self.B_compare_spot_callback)
# Some placeholder widgets, for better formatting
for j in range(6, 18):
q = QLabel(parent=self.win_left)
L_left.addWidget(q, j, 0, alignment=widget_align)
## KEYBOARD SHORTCUTS - tab right/left through frames
self.left_shortcut = QShortcut(QKeySequence(QtGui_Qt.Key_Left), self.win)
self.right_shortcut = QShortcut(QKeySequence(QtGui_Qt.Key_Right), self.win)
self.left_shortcut.activated.connect(self.tab_prev_frame)
self.right_shortcut.activated.connect(self.tab_next_frame)
## DISPLAY
self.update_image(autoRange=True, autoLevels=True, autoHistogramRange=True)
self.overlay_spots()
if "trajectory" in self.locs.columns:
self.M_color_by.setCurrentText("Trajectory")
self.M_color_by_callback()
self.win.show()
## CORE FUNCTIONS
def update_image(self, autoRange=False, autoLevels=False,
autoHistogramRange=False):
"""
Update self.imageView with the current value of self.image
and change the scatter plots if necessary.
"""
# Update the image view
self.imageView.setImage(self.image, autoRange=autoRange,
autoLevels=autoLevels, autoHistogramRange=autoHistogramRange)
def load_spots(self, frame_index=None):
"""
Load a new set of localizations.
"""
if frame_index is None:
frame_index = self.frame_slider.value()
self.locs_curr = self.locs.loc[self.locs['frame']==frame_index, :]
self.locs_pos = np.asarray(self.locs_curr[['y', 'x']])
self.locs_data = self.locs_curr.to_dict(orient='records')
def load_image(self, frame_index):
"""
Load a new image.
"""
self.image = self.imageReader.get_frame(frame_index)
def change_frame(self, frame_index):
"""
Load a new frame with a new set of spots.
"""
# Load the new image
self.load_image(frame_index)
# Load the new set of spots
self.load_spots(frame_index)
def tab_next_frame(self):
"""
Load the next frame.
"""
next_idx = int(self.frame_slider.value())
if next_idx < self.frame_slider.maximum:
next_idx += 1
self.frame_slider.setValue(next_idx)
def tab_prev_frame(self):
"""
Load the previous frame.
"""
prev_idx = int(self.frame_slider.value())
if prev_idx > self.frame_slider.minimum:
prev_idx -= 1
self.frame_slider.setValue(prev_idx)
def generate_color_spot_dict(self, color_col):
"""
From the current set of spots, generate an argument
suitable to update the scatter plot while coloring
each localization by its value of *color_col*. Usually
*color_col* is either "traj_color" or "attrib_color".
"""
symbol = self.M_symbol.currentText()
return [{'pos': tuple(self.locs_pos[i,:]+0.5), 'size': symbol_sizes[symbol],
'symbol': symbol, 'pen': {'color': self.locs_data[i][color_col], "width": pen_width},
'brush': None} for i in range(self.locs_pos.shape[0])]
def overlay_spots(self):
"""
Overlay the current set of spots onto the current image.
"""
if self.B_overlay_state:
# Get the current overlay symbol
symbol = self.M_symbol.currentText()
# Get the current coloring scheme
color_by = self.M_color_by.currentText()
# Overlay the spots
if color_by == "None":
self.scatterPlotItem.setData(pos=self.locs_pos+0.5,
data=self.locs_data, symbol=symbol,
size=symbol_sizes[symbol], **overlay_params)
elif color_by == "Trajectory":
self.scatterPlotItem.setData(
spots=self.generate_color_spot_dict("traj_color"),
data=self.locs_data
)
elif color_by == "Quantitative attribute":
self.scatterPlotItem.setData(
spots=self.generate_color_spot_dict("attrib_color"),
data=self.locs_data,
)
elif color_by == "Boolean attribute":
self.scatterPlotItem.setData(
spots=self.generate_color_spot_dict("condition_color"),
data=self.locs_data,
)
else:
self.scatterPlotItem.setData([])
# Also overlay the trajectory histories, if desired
if self.B_overlay_trails_state:
self.overlay_trails()
def generate_color_schemes(self):
"""
Generate two color schemes for this dataframe.
"""
self.n_colors = 133
# Color scheme 1: viridis
cmap = cm.get_cmap("viridis", self.n_colors)
self.colors_0 = np.array(
[mpl_colors.rgb2hex(cmap(i)[:3]) for i in range(self.n_colors)]
)
# Color scheme 2: inferno
cmap = cm.get_cmap("cool", self.n_colors)
self.colors_1 = np.array(
[mpl_colors.rgb2hex(cmap(i)[:3]) for i in range(self.n_colors)]
)
def assign_traj_colors(self):
"""
Assign the "traj_color" column of the dataframe, which assign
each trajectory a different hex color.
"""
# If the dataframe does not have a "trajectory" column, then
# all of the spots get the same color
if not "trajectory" in self.locs.columns:
print("assign_traj_colors: `trajectory` column not found in dataframe")
self.locs["traj_color"] = MASTER_COLOR
else:
self.locs["traj_color"] = self.colors_0[
(self.locs["trajectory"]*9277) % self.n_colors]
# If a spot is not assigned to a trajectory, its color is white
unassigned = self.locs["trajectory"] == -1
self.locs.loc[unassigned, "traj_color"] = "#FFFFFF"
def assign_attribute_colors(self, attrib):
"""
Assign the "color" column of the dataframe, which determines
how individual spots are colored.
"""
# Get all of the numerical values for this attribute
x = np.asarray(self.locs[attrib].astype("float64"))
sanitary = (~np.isinf(x)) & (~np.isnan(x))
# Min and max values for the color map
cmin = np.percentile(x, 1)
cmax = np.percentile(x, 95)
# Divide up the range into bins for each color
bins = np.linspace(cmin, cmax, self.n_colors-1)
# Assign each localization to one bin on the basis
# of its attribute
assignments = np.zeros(x.shape[0], dtype='int64')
assignments[sanitary] = np.digitize(x[sanitary], bins=bins)
# Generate the color indices
self.locs["attrib_color"] = self.colors_1[assignments]
# Unsanitary inputs are colored white
self.locs.loc[~sanitary, "attrib_color"] = "#FFFFFF"
def assign_condition_colors(self, condition_col):
"""
Assign the "condition_color" of the dataframe which is
keyed to the truth value of *condition_col*.
"""
indices = self.locs[condition_col].astype('int64')
self.locs["condition_color"] = condition_colors[0]
self.locs.loc[self.locs[condition_col].astype('bool'),
"condition_color"] = condition_colors[1]
def overlay_trails(self):
"""
For each trajectory running in the current frame, overlay
that trajectory on the current image.
Relies on an updated self.locs_curr.
"""
if len(self.locs_curr) == 0:
self.graphItem.setData()
elif "trajectory" in self.locs.columns and \
self.B_overlay_trails_state:
# Get the current frame index
frame_index = self.frame_slider.value()
# Get all spots before or at the current frame
T = self.tracks[self.tracks[:,0]<=frame_index, :]
# Find the minimum trajectory index present in this frame
t = T[T[:,0]==frame_index, 1].min()
# Get all trajectories that coincide with this frame
T = T[np.where(T[:,1]==t)[0][0]:,:]
# Figure out which points correspond to the same
# trajectory
indicator = (T[1:,1] - T[:-1,1]) == 0
connect_indices = np.where(indicator)[0]
adj = np.asarray([connect_indices, connect_indices+1]).T
# Overlay
self.graphItem.setData(pos=T[:,2:4], adj=adj,
pen={'color': MASTER_COLOR, 'width': pen_width}, symbol=None,
brush=None, pxMode=False)
else:
self.graphItem.setData()
## WIDGET CALLBACKS
def spot_clicked(self, plot, points):
"""
Respond to a spot being selected by the user: change
its color and print all of its associated information
to the terminal.
"""
for p in self.lastClicked:
p.resetPen()
for p in points:
print("Spot:")
print(format_dict(p.data()))
p.setPen('w', width=3)
self.lastClicked = points
def frame_slider_callback(self):
"""
Respond to a user change in the frame slider.
"""
# Get the new frame
frame_index = self.frame_slider.value()
# Load a new image and set of localizations
self.change_frame(frame_index)
# Update the image
self.update_image()
# Update the scatter plot
self.overlay_spots()
def B_overlay_callback(self):
"""
Toggle the spot overlay.
"""
self.B_overlay_state = not self.B_overlay_state
self.overlay_spots()
def M_color_by_callback(self):
"""
Change the way that the spots are colored: either None
(all the same color), "trajectory", or "attribute".
"""
color_by = self.M_color_by.currentText()
if color_by == "Quantitative attribute":
# Prompt the user to select an attribute to color by
options = [c for c in self.locs.columns if \
self.locs[c].dtype in ["int64", "float64", "uint8", \
"uint16", "float32", "uint32", "int32"]]
ex = SingleComboBoxDialog("Attribute", options,
init_value="I0", title="Choose attribute color by",
parent=self)
ex.exec_()
# Dialog accepted
if ex.result() == 1:
attrib = ex.return_val
# Dialog rejected; default to I0
else:
print("rejected; defaulting to I0")
attrib = "I0"
# Generate the color indices
self.assign_attribute_colors(attrib)
# Update the current set of localizations
self.load_spots(self.frame_slider.value())
elif color_by == "Boolean attribute":
self.assign_attribute_colors(self.M_condition.currentText())
self.overlay_spots()
else:
pass
# Update the scatter plot
self.overlay_spots()
def M_symbol_callback(self):
"""
Change the spot overlay symbol.
"""
self.overlay_spots()
def B_overlay_trails_callback(self):
"""
Show the history of each trajectory on the raw image.
"""
self.B_overlay_trails_state = not self.B_overlay_trails_state
# Do nothing if these are not trajectories
if not "trajectory" in self.locs.columns:
return
# Else overlay the trajectory histories
self.overlay_trails()
def B_create_condition_callback(self):
"""
Launch a sub-GUI to generate a Boolean attribute on
from one of the spot columns.
"""
# Prompt the user to create a condition
ex = ConditionDialog(self.locs, parent=self)
ex.exec()
# Accepted - unpack result
if ex.result() == 1:
bounds, col = ex.return_val
l_bound, u_bound = bounds
# Add this as an option
condition_name = '%s_condition' % col
if condition_name not in self.locs.columns:
self.M_condition.QComboBox.addItems([condition_name])
# Create a new binary column on the dataframe
self.locs[condition_name] = np.logical_and(
self.locs[col]>=l_bound,
self.locs[col]<=u_bound,
)
print("%d/%d localizations in condition %s" % (
self.locs[condition_name].sum(),
len(self.locs),
condition_name
))
# Update plots, assuming that the user wants to see the
# result immediately
self.M_condition.QComboBox.setCurrentText(condition_name)
self.M_color_by.QComboBox.setCurrentText("Boolean attribute")
self.assign_condition_colors(condition_name)
self.load_spots()
self.overlay_spots()
def M_condition_callback(self):
"""
Select the current Boolean attribute to use for determining
color when using the "Boolean attribute" option in M_color_by.
"""
# Get the new condition name
c = self.M_condition.currentText()
# Assign each localization a color depending on its value
# with this value
self.assign_condition_colors(c)
# Update the plots
self.load_spots()
self.overlay_spots()
def B_compare_spot_callback(self):
"""
Launch a subwindow that shows a grid of spots in the current
frame and subsequent frames.
This callback has two behaviors, depending on the current
state of self.M_color_by. If we're color by a Boolean attribute,
then launch a ImageSubpositionCompare window. Else launch a
ImageSubpositionWindow. The former compares two sets of spots
side-by-side, while the second is just a single grid of spots.
"""
if self.M_color_by.currentText() == "Boolean attribute":
# Size of image grid
N = 8
# Get the current Boolean attribute column
col = self.M_condition.currentText()
# Get as many spots as we can to fill this image grid
frame_index = self.frame_slider.value()
positions_false = []
positions_true = []
images = []
while frame_index<self.imageReader.n_frames and \
(sum([i.shape[0] for i in positions_false])<N**2 or
(sum([i.shape[0] for i in positions_true])<N**2)):
im = self.imageReader.get_frame(frame_index)
frame_locs = self.locs.loc[
self.locs['frame']==frame_index,
['y', 'x', col],
]
frame_locs_true = np.asarray(frame_locs.loc[
frame_locs[col], ['y', 'x']]).astype(np.int64)
frame_locs_false = np.asarray(frame_locs.loc[
~frame_locs[col], ['y', 'x']]).astype(np.int64)
images.append(im)
positions_true.append(frame_locs_true)
positions_false.append(frame_locs_false)
frame_index += 1
# Launch a ImageSubpositionCompare instance
ex = ImageSubpositionCompare(images, positions_true, positions_false,
w=15, N=N, colors=condition_colors, parent=self)
else:
# Size of image grid
N = 10
# Get as many spots as we can to fill this image grid
frame_index = self.frame_slider.value()
positions = []
images = []
while sum([i.shape[0] for i in positions])<N**2 and \
frame_index<self.imageReader.n_frames:
im = self.imageReader.get_frame(frame_index)
frame_locs = np.asarray(self.locs.loc[
self.locs['frame']==frame_index, ['y', 'x']]).astype(np.int64)
images.append(im)
positions.append(frame_locs)
frame_index += 1
# Launch an ImageSubpositionWindow
ex = ImageSubpositionWindow(images, positions,
w=15, N=N, parent=self)