def __init__(self):
super(MainWindow, self).__init__()
self.resize(500, 40)
self.setWindowTitle("Key Frame View")
self.keyPanel = KeyFramePanel(None)
dataModel = DataModel(dataContainer=DemoData(50), prefetchSize=0)
transModel = TransformModel()
transModel.setModel(dataModel)
transModel.setValueScale(0, 200)
dataModel.setPos(2)
self.keyPanel.connect_to_transform(transModel)
k = KeyFrameList()
k.addItem(KeyFrame(0.))
k.addItem(KeyFrame(1.))
self.keyPanel.setModel(k)
self.setCentralWidget(self.keyPanel)
self.setStyleSheet("background-color:black;color:white")
def __init__(self):
super(MainWindow,self).__init__()
self.resize(500, 40)
self.setWindowTitle("Key Frame View")
self.keyPanel = KeyFramePanel(None)
dataModel = DataModel(dataContainer = DemoData(50),prefetchSize = 0)
transModel = TransformModel()
transModel.setModel(dataModel)
transModel.setValueScale(0,200)
dataModel.setPos(2)
self.keyPanel.connect_to_transform(transModel)
k = KeyFrameList()
k.addItem(KeyFrame(0.))
k.addItem(KeyFrame(1.))
self.keyPanel.setModel(k)
self.setCentralWidget(self.keyPanel)
self.setStyleSheet("background-color:black;color:white")
def openFile(self,e):
# path = QtWidgets.QFileDialog.getOpenFileName(self, 'Open Path (File or Folder)',
# '.', selectedFilter='*.tif')
f = QtWidgets.QFileDialog()
f.setWindowTitle('Open Path (File or Folder)')
f.setFileMode(QtWidgets.QFileDialog.ExistingFile & QtWidgets.QFileDialog.Directory)
f.exec_()
path = f.selectedFiles()
if len(path)==0:
return
path = str(path[0])
if path:
try:
if self.glWidget.dataModel:
self.glWidget.dataModel.loadFromPath(path,
prefetchSize = self.glWidget.N_PREFETCH)
else:
self.glWidget.setModel(DataModel.fromPath(path,
prefetchSize = self.glWidget.N_PREFETCH))
except Exception as e:
mbox = QtWidgets.QMessageBox()
mbox.setText(str(e))
mbox.setIcon(QtWidgets.QMessageBox.Warning)
mbox.exec_()
def dropEvent(self, event):
def _url_to_path(url):
path = url.toLocalFile()
if spimagine.config.__SYSTEM_DARWIN__:
path = spimagine.config._parseFileNameFix(path)
return path
self.setCursor(QtCore.Qt.BusyCursor)
urls = event.mimeData().urls()
if len(urls) == 0:
return
elif len(urls) == 1:
path = _url_to_path(urls[0])
elif len(urls) > 1:
path = tuple(_url_to_path(url) for url in urls)
try:
if self.dataModel:
self.dataModel.loadFromPath(path, prefetchSize=self.N_PREFETCH)
else:
self.setModel(
DataModel.fromPath(path, prefetchSize=self.N_PREFETCH))
self.setCursor(QtCore.Qt.ArrowCursor)
except Exception as e:
QtWidgets.QMessageBox.warning(self, "",
"Error loading Data:\n %s" % str(e))
def test_surface():
from spimagine import DataModel, NumpyData, DemoData
from spimagine.gui.mesh import SphericalMesh
app = QtWidgets.QApplication(sys.argv)
win = MainWidget()
x = np.linspace(-1, 1, 128)
Z, Y, X = np.meshgrid(x, x, x)
d = np.exp(-10 * X**2)
win.setModel(DataModel(DemoData()))
# win.glWidget.add_surface_ellipsoid((1.,0,0),
# (.2,.2,.2),
# facecolor = (1.,.3,.1,.5),
# edgecolor = (1.,1.,1.,.2),
# Nphi =20, Ntheta=10)
# win.glWidget.add_mesh(SphericalMesh(facecolor = (1.,1.,1.),
# edgecolor = None))
win.show()
win.raise_()
sys.exit(app.exec_())
def dropEvent(self, event):
def _url_to_path(url):
path = url.toLocalFile()
if spimagine.config.__SYSTEM_DARWIN__:
path = spimagine.config._parseFileNameFix(path)
return path
self.setCursor(QtCore.Qt.BusyCursor)
urls = event.mimeData().urls()
if len(urls) == 0:
return
elif len(urls) == 1:
path = _url_to_path(urls[0])
elif len(urls) > 1:
path = tuple(_url_to_path(url) for url in urls)
try:
if self.dataModel:
self.dataModel.loadFromPath(path, prefetchSize=self.N_PREFETCH)
else:
self.setModel(DataModel.fromPath(path, prefetchSize=self.N_PREFETCH))
self.setCursor(QtCore.Qt.ArrowCursor)
except Exception as e:
QtWidgets.QMessageBox.warning(self, "", "Error loading Data:\n %s" % str(e))
def test_surface():
from spimagine import DataModel, DemoData
app = QtWidgets.QApplication(sys.argv)
win = GLWidget(size=QtCore.QSize(800, 600))
win.setModel(DataModel(DemoData()))
# win.add_surface_sphere((0,0,0), 1., facecolor = (.0,.3,1.,.5),
# Nphi = 30, Ntheta=20)
# win.add_mesh(SphericalMesh(r = .8,
# facecolor = (1.,0.,0.),
# #edgecolor = (1.,1.,1.),
# edgecolor = None,
# alpha = .3))
# win.add_mesh(EllipsoidMesh(rs = (.3,.6,.6),
# pos = (0,0,-.5),
#
# facecolor = (0.,1.,1.),
# #edgecolor = (1.,1.,1.),
# edgecolor = None,
# alpha = .4))
#
win.show()
win.raise_()
sys.exit(app.exec_())
def test_sphere():
from spimagine import DataModel, NumpyData, SpimData, TiffData
app = QtWidgets.QApplication(sys.argv)
win = GLWidget(size=QtCore.QSize(500, 500), interpolation="nearest")
x = np.linspace(-1, 1, 64)
Z, Y, X = np.meshgrid(x, x, x)
# R = sqrt(Z**2+Y**2+(X-.35)**2)
# R2 = sqrt(Z**2+Y**2+(X+.35)**2)
# d = 100.*exp(-10*R**2)+.0*np.random.normal(0,1.,X.shape)
# d += 100.*exp(-10*R2**2)+.0*np.random.normal(0,1.,X.shape)
Ns = 5
r = .6
phi = np.linspace(0, 2 * np.pi, Ns + 1)[:-1]
d = np.zeros_like(X)
for p in phi:
d += 100. * np.exp(-10 * (Z**2 + (Y - r * np.sin(p))**2 +
(X - r * np.cos(p))**2))
win.setModel(DataModel(NumpyData(d)))
win.transform.setValueScale(0, 40)
win.show()
win.raise_()
sys.exit(app.exec_())
def dropEvent(self, event):
for url in event.mimeData().urls():
path = url.toLocalFile().toLocal8Bit().data()
if self.dataModel:
self.dataModel.loadFromPath(path, prefetchSize=self.N_PREFETCH)
else:
self.setModel(DataModel.fromPath(path, prefetchSize=self.N_PREFETCH))
def test_sphere():
from spimagine import DataModel, NumpyData
x = np.linspace(-1, 1, 32)
Z, Y, X = np.meshgrid(x, x, x)
# R = sqrt(Z**2+Y**2+(X-.35)**2)
# R2 = sqrt(Z**2+Y**2+(X+.35)**2)
# d = 100.*exp(-10*R**2)+.0*np.random.normal(0,1.,X.shape)
# d += 100.*exp(-10*R2**2)+.0*np.random.normal(0,1.,X.shape)
Ns = 5
r = .6
phi = np.linspace(0, 2 * np.pi, Ns + 1)[:-1]
d = np.zeros_like(X)
for p in phi:
d += 200. * np.exp(-10 * (Z**2 + (Y - r * np.sin(p))**2 +
(X - r * np.cos(p))**2))
app = QtWidgets.QApplication(sys.argv)
win = MainWidget()
win.setModel(DataModel(NumpyData(d)))
# win.glWidget.transform.setIso(True)
# win.glWidget.transform.setValueScale(0,40)
# win.saveFile(None)
win.show()
win.raise_()
sys.exit(app.exec_())
def dropEvent(self, event):
for url in event.mimeData().urls():
path = url.toLocalFile().toLocal8Bit().data()
if self.dataModel:
self.dataModel.loadFromPath(path, prefetchSize=self.N_PREFETCH)
else:
self.setModel(DataModel.fromPath(path, prefetchSize=self.N_PREFETCH))
def openFile(self, e):
# path = QtWidgets.QFileDialog.getOpenFileName(self, 'Open Path (File or Folder)',
# '.', selectedFilter='*.tif')
f = QtWidgets.QFileDialog()
f.setWindowTitle('Open Path (File or Folder)')
f.setFileMode(QtWidgets.QFileDialog.ExistingFile
& QtWidgets.QFileDialog.Directory)
f.exec_()
path = f.selectedFiles()
if len(path) == 0:
return
path = str(path[0])
if path:
try:
if self.glWidget.dataModel:
self.glWidget.dataModel.loadFromPath(
path, prefetchSize=self.glWidget.N_PREFETCH)
else:
self.glWidget.setModel(
DataModel.fromPath(
path, prefetchSize=self.glWidget.N_PREFETCH))
except Exception as e:
mbox = QtWidgets.QMessageBox()
mbox.setText(str(e))
mbox.setIcon(QtWidgets.QMessageBox.Warning)
mbox.exec_()
def test_demo_simple():
from spimagine import DataModel, DemoData
app = QtWidgets.QApplication(sys.argv)
win = GLWidget(size=QtCore.QSize(800, 800))
win.setModel(DataModel(DemoData()))
win.show()
win.raise_()
sys.exit(app.exec_())
def test_demo():
from data_model import DataModel, DemoData, SpimData, TiffData, NumpyData
app = QtWidgets.QApplication(sys.argv)
win = GLWidget(size=QtCore.QSize(800, 800))
win.setModel(DataModel(DemoData()))
win.show()
win.raise_()
sys.exit(app.exec_())
def test_empty():
from spimagine import DataModel, NumpyData, SpimData, TiffData
app = QtWidgets.QApplication(sys.argv)
win = MainWidget()
d = np.zeros((600, ) * 3, np.float32)
d[0, 0, 0] = 1.
win.setModel(DataModel(NumpyData(d)))
win.show()
win.raise_()
sys.exit(app.exec_())
def dropEvent(self, event):
for url in event.mimeData().urls():
# path = url.toLocalFile().toLocal8Bit().data()
path = url.toLocalFile()
if spimagine.config.__SYSTEM_DARWIN__:
path = spimagine.config._parseFileNameFix(path)
self.setCursor(QtCore.Qt.BusyCursor)
if self.dataModel:
self.dataModel.loadFromPath(path, prefetchSize=self.N_PREFETCH)
else:
self.setModel(DataModel.fromPath(path, prefetchSize=self.N_PREFETCH))
self.setCursor(QtCore.Qt.ArrowCursor)
def test_empty():
from spimagine import DataModel, NumpyData, SpimData, TiffData
app = QtWidgets.QApplication(sys.argv)
win = GLWidget(size=QtCore.QSize(1000, 1000))
d = np.zeros((800, ) * 3, np.float32)
d[0, 0, 0] = 1.
win.show()
win.raise_()
QtCore.QThread.msleep(1000)
win.setModel(DataModel(NumpyData(d)))
sys.exit(app.exec_())
def volshow(data,
autoscale=True,
stackUnits=[1., 1., 1.],
blocking=False,
cmap=None,
interpolation="linear",
show_window=True,
raise_window=True):
"""
class to visualize 3d/4d data
data can be
- a 3d/4d numpy array of dimensions (z,y,x) or (t,z,y,x)
e.g.
volshow( randint(0,10,(10, 20,30,40) )
- an instance of a class derived from the abstract bass class GenericData
e.g.
from spimagine.models.data_model import GenericData
class myData(GenericData):
def __getitem__(self,i):
return (100*i+3)*np.ones((100,100,100))
def size(self):
return (4,100,100,100)
volshow(myData())
or
from spimagine.data_model import DataModel
volshow(DataModel(dataContainer=myData(), prefetchSize= 5)
Parameters
----------
data: ndarray
the volumetric data to render, 3d or 4d
autoscale: boolean
autoscales the data
stackUnits: tuple
the voxel dimensions (dx, dy, dz)
blocking: boolean
if true, starts the qt event loop and waits till finished
(use this e.g. when running from outside ipython)
cmap: str
the colormap to use
available colormaps: cmap = ["viridis", "coolwarm","jet","hot","grays"]
if None, then the default one is used
interpolation: str
the interpolation used for rendering/slice views
"linear" or "nearest"
raise_window: boolean
if true, raises the window
Returns
-------
the widget w
"""
logger.debug("volshow")
logger.debug("volshow: getCurrentApp")
app = getCurrentApp()
from time import time
t = time()
# if isinstance(data,GenericData):
if isinstance(data, DataModel):
m = data
elif hasattr(data, "stackUnits"):
m = DataModel(data)
else:
if not isinstance(data, np.ndarray):
data = np.array(data)
if autoscale:
data = _rescale(data, 10000, 0)
if not data.dtype.type in VolumeRenderer.dtypes:
data = data.astype(np.float32, copy=False)
m = DataModel(NumpyData(data))
logger.debug("create model: %s s " % (time() - t))
t = time()
# check whether there are already open windows, if not create one
try:
num, window = [(n, w) for n, w in six.iteritems(app.volfigs)][-1]
except:
num = 1
window = volfig(num, interpolation=interpolation)
logger.debug("volfig: %s s " % (time() - t))
t = time()
window.setModel(m)
logger.debug("set model: %s s" % (time() - t))
if cmap is None or cmap not in spimagine.config.__COLORMAPDICT__:
cmap = spimagine.config.__DEFAULTCOLORMAP__
window.glWidget.set_colormap(cmap)
window.glWidget.transform.setStackUnits(*stackUnits)
if show_window:
window.show()
if raise_window:
window.raise_window()
if blocking:
getCurrentApp().exec_()
else:
return window
def setModel(self, dataModel):
self.glSliceWidget.setModel(dataModel)
# def wheelEvent(self, event):
# self.sliderSlice.wheelEvent(event)
if __name__ == '__main__':
from spimagine import DemoData, NumpyData
app = QtWidgets.QApplication(sys.argv)
# win = GLSliceWidget(size=QtCore.QSize(500,500))
win = SliceWidget(size=QtCore.QSize(500, 500), interp=False)
d = random.uniform(0, 1, (10, 20, 30))
win.setModel(DataModel(NumpyData(d)))
# win.setModel(DataModel(DemoData()))
win.transform.setMax(1.)
# win.transform.setPerspective(True)
win.show()
win.raise_()
sys.exit(app.exec_())
def main():
parser = argparse.ArgumentParser(description='spimagine rendering application ')
parser.add_argument('fname',
type=str,
nargs='*',
help='the files/folder to open (e.g. tif, folder of tif) ',
default = None)
parser.add_argument('-p',
dest='prefetch',
type = int,
default=0,
help='prefetch size (should not be negative, e.g. -p 2)')
parser.add_argument('-u',
dest='units',
nargs = 3,
type=float,
default=[1.,1.,1.],
help='voxel units')
parser.add_argument('-D',
action='store_true',
help="output DEBUG messages")
parser.add_argument('-v',"--verbose",
action='store_true',
help="output DEBUG messages")
try:
args = parser.parse_args()
except Exception as e:
print(e)
parser.print_help()
sys.exit(0)
logger = logging.getLogger("spimagine")
if args.D or args.verbose:
logger.setLevel(logging.DEBUG)
# if sys.platform.startswith("win"):
# QtWidgets.QApplication.setStyle(QtWidgets.QStyleFactory.create("CleanLooks"))
# print(QtWidgets.QStyleFactory.create("Fusion"))
# QtWidgets.QApplication.setStyle(QtWidgets.QStyleFactory.create("Fusion"))
# QtWidgets.QApplication.setStyle(QtWidgets.QStyleFactory.create(QtWidgets.QStyleFactory.keys()[1]))
app = QtWidgets.QApplication(sys.argv)
logger.debug("available qt styles: %s " % str(QtWidgets.QStyleFactory.keys()))
logger.debug("used qt styles: %s " % app.style().metaObject().className())
#splash screen
pixmap = QtGui.QPixmap(absPath('../gui/images/splash.png'))
splash = QtWidgets.QSplashScreen(pixmap, QtCore.Qt.WindowStaysOnTopHint)
splash.setMask(pixmap.mask())
splash.show()
app.processEvents()
import spimagine
from spimagine.gui.mainwidget import MainWidget
from spimagine.models.data_model import DemoData, DataModel
app.setWindowIcon(QtGui.QIcon(absPath('../gui/images/spimagine.png')))
win = MainWidget()
win.resize(spimagine.config.__DEFAULT_WIDTH__, spimagine.config.__DEFAULT_HEIGHT__)
splash.hide()
if args.fname:
if len(args.fname)==1:
win.setModel(DataModel.fromPath(args.fname[0]))
else:
win.setModel(DataModel.fromPath(args.fname))
else:
win.setModel(DataModel(DemoData()))
win.transform.setStackUnits(*args.units)
win.show()
win.raise_window()
splash.finish(win)
sys.exit(app.exec_())
def main():
parser = argparse.ArgumentParser(
description='spimagine rendering application ')
parser.add_argument(
'fname',
type=str,
nargs='*',
help='the files/folder to open (e.g. tif, folder of tif) ',
default=None)
parser.add_argument(
'-p',
dest='prefetch',
type=int,
default=0,
help='prefetch size (should not be negative, e.g. -p 2)')
parser.add_argument('-u',
dest='units',
nargs=3,
type=float,
default=[1., 1., 1.],
help='voxel units')
parser.add_argument('-D',
action='store_true',
help="output DEBUG messages")
parser.add_argument('-v',
"--verbose",
action='store_true',
help="output DEBUG messages")
try:
args = parser.parse_args()
except Exception as e:
print(e)
parser.print_help()
sys.exit(0)
logger = logging.getLogger("spimagine")
if args.D or args.verbose:
logger.setLevel(logging.DEBUG)
# if sys.platform.startswith("win"):
# QtWidgets.QApplication.setStyle(QtWidgets.QStyleFactory.create("CleanLooks"))
# print(QtWidgets.QStyleFactory.create("Fusion"))
# QtWidgets.QApplication.setStyle(QtWidgets.QStyleFactory.create("Fusion"))
# QtWidgets.QApplication.setStyle(QtWidgets.QStyleFactory.create(QtWidgets.QStyleFactory.keys()[1]))
app = QtWidgets.QApplication(sys.argv)
logger.debug("available qt styles: %s " %
str(QtWidgets.QStyleFactory.keys()))
logger.debug("used qt styles: %s " % app.style().metaObject().className())
#splash screen
pixmap = QtGui.QPixmap(absPath('../gui/images/splash.png'))
splash = QtWidgets.QSplashScreen(pixmap, QtCore.Qt.WindowStaysOnTopHint)
splash.setMask(pixmap.mask())
splash.show()
app.processEvents()
import spimagine
from spimagine.gui.mainwidget import MainWidget
from spimagine.models.data_model import DemoData, DataModel
app.setWindowIcon(QtGui.QIcon(absPath('../gui/images/spimagine.png')))
win = MainWidget()
win.resize(spimagine.config.__DEFAULT_WIDTH__,
spimagine.config.__DEFAULT_HEIGHT__)
splash.hide()
if args.fname:
if len(args.fname) == 1:
win.setModel(DataModel.fromPath(args.fname[0]))
else:
win.setModel(DataModel.fromPath(args.fname))
else:
win.setModel(DataModel(DemoData()))
win.transform.setStackUnits(*args.units)
win.show()
win.raise_window()
splash.finish(win)
sys.exit(app.exec_())
