def showLoadDialog(self):
"""
This slot brings up the load dialog and retrieves the file name.
If the file name is valid, it loads the image stack using the load method.
"""
fname = self.lasagna.showFileLoadDialog(fileFilter="LSM (*.lsm)")
if fname is None:
return
color_order = preferences.readPreference('colorOrder')
if os.path.isfile(fname):
im = tifffile.imread(str(fname))
print("Found LSM stack with dimensions:")
print(im.shape)
for i in range(im.shape[2]):
stack = im[0, :, i, :, :]
obj_name = "layer_%d" % (i + 1)
self.lasagna.addIngredient(objectName=obj_name,
kind='imagestack',
data=stack,
fname=fname)
self.lasagna.returnIngredientByName(
obj_name).addToPlots() # Add item to all three 2D plots
print("Adding '{}' layer".format(color_order[i]))
self.lasagna.returnIngredientByName(
obj_name).lut = color_order[i]
self.lasagna.initialiseAxes()
else:
self.lasagna.statusBar.showMessage(
"Unable to find {}".format(fname))
def chooseTransform_slot(self, fname_to_choose=False):
"""
Choose the transform file to use
can optionally load a specific file name (used for de-bugging)
"""
if not fname_to_choose:
file_filter = "Images (*.txt)"
fname_to_choose = QtGui.QFileDialog.getOpenFileName(
self, 'Choose transform',
preferences.readPreference('lastLoadDir'), file_filter)
fname_to_choose = str(fname_to_choose)
if os.path.exists(fname_to_choose):
self.transformPath = fname_to_choose
else:
self.transformPath = ''
# TODO: make an alert box for this case
print("that file does not exits")
self.checkIfReadyToRun()
preferences.preferenceWriter(
'lastLoadDir',
lasagna.utils.path_utils.stripTrailingFileFromPath(
fname_to_choose))
self.transformName_label.setText(
fname_to_choose.split(os.path.sep)[-1])
def __init__(self,
parent=None,
data=None,
fnameAbsPath="",
enable=True,
objectName=""):
super(sparsepoints, self).__init__(parent,
data,
fnameAbsPath,
enable,
objectName,
pgObject="ScatterPlotItem")
# Choose symbols from preferences file. TODO: in future could increment through so successive ingredients have different symbols and colors
self.symbol = preferences.readPreference("symbolOrder")[0]
self.symbolSize = int(self.parent.markerSize_spinBox.value())
self.alpha = int(self.parent.markerAlpha_spinBox.value())
self.lineWidth = None # Not used right now
self.build_model_for_list(objectName)
self.model = self.parent.points_Model
self.addToList()
# Set the colour of the object based on how many items are already present
# TODO: duplicate code with lines.py
number_of_colors = 6
this_number = (self.parent.points_Model.rowCount() -
1) % number_of_colors # FIXME: rename
cm_subsection = linspace(0, 1, number_of_colors)
colors = [cm.jet(x) for x in cm_subsection]
color = colors[this_number]
self.color = [color[0] * 255, color[1] * 255, color[2] * 255]
def __init__(self,
parent=None,
data=None,
fnameAbsPath="",
enable=True,
objectName=""):
super(lines, self).__init__(parent,
data,
fnameAbsPath,
enable,
objectName,
pgObject="PlotCurveItem")
# Choose symbols from preferences file.
# TODO: read symbols from GUI
self.symbol = preferences.readPreference("symbolOrder")[0]
self.symbolSize = int(self.parent.markerSize_spinBox.value())
self.alpha = int(self.parent.markerAlpha_spinBox.value())
self.lineWidth = int(self.parent.lineWidth_spinBox.value())
self.build_model_for_list(objectName)
self.model = self.parent.points_Model
self.addToList()
# Set the colour of the object based on how many items are already present
# TODO: duplicate code with sparsepoints.py
number_of_colors = 6
this_number = (self.parent.points_Model.rowCount() -
1) % number_of_colors # FIXME: rename
cm_subsection = linspace(0, 1, number_of_colors)
colors = [cm.jet(x) for x in cm_subsection]
color = colors[this_number]
self.color = [color[0] * 255, color[1] * 255, color[2] * 255]
def __init__(self,
thisPlotWidget,
lasagna_serving,
axisName='',
minMax=(0, 1500),
axisRatio=1,
axisToPlot=0):
"""
thisPlotWidget - the PlotWidget to which we will add the axes
minMax - the minimum and maximum values of the plotted image.
axisRatio - the voxel size ratio along the x and y axes. 1 means square voxels.
axisToPlot - the dimension along which we are slicing the data.
"""
# Create properties
self.axisToPlot = axisToPlot # the axis in 3D space that this view correponds to
self.axisName = axisName
# We can link this projection to two others
self.linkedXprojection = None
self.linkedYprojection = None
print("Creating axis at " + str(thisPlotWidget.objectName()))
self.view = thisPlotWidget # This should target the axes to a particular plot widget
if preferences.readPreference('hideZoomResetButtonOnImageAxes'):
self.view.hideButtons()
if preferences.readPreference('hideAxes'):
self.view.hideAxis('left')
self.view.hideAxis('bottom')
self.view.setAspectLocked(True, axisRatio)
# Loop through the ingredients list and add them to the ViewBox
self.lasagna = lasagna_serving
self.items = [
] # a list of added plot items TODO: check if we really need this
self.addItemsToPlotWidget(self.lasagna.ingredientList)
# The currently plotted slice
self.currentSlice = None
# Link the progressLayer signal to a slot that will move through image layers as the wheel is turned
self.view.getViewBox().progressLayer.connect(self.wheel_layer_slot)
def get_voxel_spacing(fname, fall_back_mode=False):
"""
Attempts to get the voxel spacing in all three dimensions. This allows us to set the axis
ratios automatically. TODO: Currently this will only work for MHD files, but we may be able
to swing something for TIFFs (e.g. by creating Icy-like metadata files)
"""
if fname.lower().endswith(".mhd"):
return mhd_get_ratios(fname)
if fname.lower().endswith(".nrrd") or fname.lower().endswith(".nrd"):
return nrrd_get_ratios(fname)
else:
return preferences.readPreference("defaultAxisRatios") # defaults
def mhd_get_ratios(fname):
"""
Get relative axis ratios from MHD file defined by fname
"""
if not check_file_exists(fname, mhd_get_ratios):
return
try:
# Attempt to use the vtk module to read the element spacing
imp.find_module("vtk")
import vtk
imr = vtk.vtkMetaImageReader()
imr.SetFileName(fname)
imr.Update()
im = imr.GetOutput()
spacing = im.GetSpacing()
except ImportError:
# If the vtk module fails, we try to read the spacing using the built-in reader
info = mhd_read_header_file(fname)
if "elementspacing" in info:
spacing = info["elementspacing"]
else:
print(
"Failed to find spacing info in MHA file. Using default axis length values"
)
return preferences.readPreference("defaultAxisRatios") # defaults
if not spacing:
print(
"Failed to find spacing valid spacing info in MHA file. Using default axis length values"
)
return preferences.readPreference("defaultAxisRatios") # defaults
return spacing_to_ratio(spacing)
def loadOther_pushButton_slot(self, fnameToLoad=False):
"""
Load a user-selected atlas file but use the labels from the ARA in the drop-down box.
Can optionally load a specific file name (used for de-bugging)
"""
if not fnameToLoad:
file_filter = "Images (*.mhd *.mha *.tiff *.tif *.nrrd)"
fnameToLoad = QtGui.QFileDialog.getOpenFileName(
self, 'Open file', preferences.readPreference('lastLoadDir'),
file_filter)
fnameToLoad = str(fnameToLoad[0]) # tuple with filter as 2nd value
# re-load labels
selected_name = str(
self.araName_comboBox.itemText(
self.araName_comboBox.currentIndex()))
paths = self.paths[selected_name]
self.data['labels'] = self.loadLabels(paths['labels'])
# load the selected atlas (without displaying it)
self.data['atlas'] = image_stack_loader.load_stack(fnameToLoad)
self.data['currentlyLoadedAtlasName'] = fnameToLoad.split(
os.path.sep)[-1]
def get_fname(self):
fnames = QtGui.QFileDialog.getOpenFileNames(
self, 'Open file', preferences.readPreference('lastLoadDir'),
self.fileFilter)[0]
# getOpenFileNames returns a tuple of (file_list, filter). Ignore the filter
self.FileListTextEdit.setText('\n'.join(fnames))