alexblaessle / pyfrap Goto Github PK
View Code? Open in Web Editor NEWPyFRAP: A Python based FRAP analysis tool box
License: GNU General Public License v3.0
PyFRAP: A Python based FRAP analysis tool box
License: GNU General Public License v3.0
KeyPressEvent callback is somehow now working. Error message:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_qt5.py", line 315, in keyPressEvent
FigureCanvasBase.key_press_event(self, key)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/backend_bases.py", line 1833, in key_press_event
self.callbacks.process(s, event)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/cbook.py", line 540, in process
proxy(*args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/cbook.py", line 415, in __call__
return mtd(*args, **kwargs)
TypeError: keyPressed() takes exactly 1 argument (2 given)
When trying to prepare .czi files to create an embryo file:
"The system cannot find the path specified.
mv: cannot stat '\f......': No such file or directory"
Might need to open text file differently when writing to the file. Something like:
with open(fn,'w') as f:
....
Traceback (most recent call last):
File "C:\Users\hpreiss\AppData\Local\Continuum\Anaconda2\lib\site-packages\pyfrp\gui\pyfrp_app.py", line 1416, in openWizard
self.newEmbryo()
File "C:\Users\hpreiss\AppData\Local\Continuum\Anaconda2\lib\site-packages\pyfrp\gui\pyfrp_app.py", line 1243, in newEmbryo
self.editGeometry()
File "C:\Users\hpreiss\AppData\Local\Continuum\Anaconda2\lib\site-packages\pyfrp\gui\pyfrp_app.py", line 1590, in editGeometry
ret=pyfrp_gui_geometry_dialogs.zebrafishDomeStageDialog(currEmbryo.geometry,self).exec_()
File "C:\Users\hpreiss\AppData\Local\Continuum\Anaconda2\lib\site-packages\pyfrp\gui\pyfrp_gui_geometry_dialogs.py", line 245, in init
super(zebrafishDomeStageDialog,self).init(geometry,parent)
File "C:\Users\hpreiss\AppData\Local\Continuum\Anaconda2\lib\site-packages\pyfrp\gui\pyfrp_gui_geometry_dialogs.py", line 136, in init
self.drawGeometry()
File "C:\Users\hpreiss\AppData\Local\Continuum\Anaconda2\lib\site-packages\pyfrp\gui\pyfrp_gui_geometry_dialogs.py", line 223, in drawGeometry
self.geometry.plotGeometry(ax=self.ax,ann=self.ann)
File "C:\Users\hpreiss\AppData\Local\Continuum\Anaconda2\lib\site-packages\pyfrp\subclasses\pyfrp_geometry.py", line 333, in plotGeometry
domain.draw(ax=ax,color=color,ann=ann)
File "C:\Users\hpreiss\AppData\Local\Continuum\Anaconda2\lib\site-packages\pyfrp\modules\pyfrp_gmsh_geometry.py", line 978, in draw
ax=pyfrp_vtk_module.renderVTK(ax)
File "C:\Users\hpreiss\AppData\Local\Continuum\Anaconda2\lib\site-packages\pyfrp\modules\pyfrp_vtk_module.py", line 112, in renderVTK
if renderer.GetRenderWindow()==None:
AttributeError: 'Axes3DSubplot' object has no attribute 'GetRenderWindow'
Error traceback below after clicking done basic canvas dialog. No pop-up(s) appear thereafter to continue.
Thanks
Traceback (most recent call last):
File "/home/osboxes/.local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_app.py", line 1561, in openWizard
ret=self.newEmbryo()
File "/home/osboxes/.local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_app.py", line 1365, in newEmbryo
ret=self.editEmbryo()
File "/home/osboxes/.local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_app.py", line 1429, in editEmbryo
self.updatePropBar()
File "/home/osboxes/.local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_app.py", line 1137, in updatePropBar
self.showObjPropsInBar(self.currObj)
File "/home/osboxes/.local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_app.py", line 1115, in showObjPropsInBar
if isinstance(vars(obj)[str(item)],(int,float,str)) or vars(obj)[str(item)]==None:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
I pulled the most recent version and I now get the following error in PyFRAP when building the embryo:
"WARNING (mkdir): Could not create folder \\...\...\...\David\Data\FRAP\Sqt-GFP_PyFRAP\2017_04_11\ .
WARNING (updateFileList): There are no files of type tif in \\...\...\...\David\Data\FRAP\Sqt-GFP_PyFRAP\2017_04_11\recover/ . This can lead to problems."
In the terminal it says "The System cannot find the path specified."
EDIT: Actually, I think this is not a Windows problem only. I get the same under Ubuntu.
after choosing folder embryo data, embryo creationbutton only creates new folders but no tiffs
WARNING:There are no files of type tif in . This can lead to problems.
After readjusting the mesh volSize via Simulation->Mesh->Mesh Settings, we get the following error:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/pyfrp/gui/pyfrp_app.py", line 1756, in generateMesh
self.editMesh()
File "/usr/local/lib/python2.7/dist-packages/pyfrp/gui/pyfrp_app.py", line 1742, in editMesh
ret=pyfrp_gui_mesh_dialogs.meshSettingsDialog(currEmbryo.simulation.mesh,self).exec_()
File "/usr/local/lib/python2.7/dist-packages/pyfrp/gui/pyfrp_gui_mesh_dialogs.py", line 72, in __init__
self.updateFnMeshLbl()
File "/usr/local/lib/python2.7/dist-packages/pyfrp/gui/pyfrp_gui_mesh_dialogs.py", line 127, in updateFnMeshLbl
self.lblFnMeshVal.setText("..."+self.mesh.fnMesh[-self.nCharDisplayed:])
TypeError: 'GmshImporter3D' object has no attribute '__getitem__'
which clearly points that mesh.fnMesh
now contains what should be in mesh.mesh
. This either happens in pyfrp_mesh
class itself or in settings dialog.
It seems that in general QThreads block any other interaction with the GUI. It actually already blocks the initiation of the __init__
of the progressbar dialog. It might be worthwile to introduce a thread.sleep
at the start of thread initiation.
File "/usr/local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_app.py", line 2084, in summarizeMolecule
self.selectFits()
File "/usr/local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_app.py", line 2052, in selectFits
ret=pyfrp_gui_statistics_dialogs.fitSelector(self.currMolecule,True,self).exec_()
File "/usr/local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_gui_statistics_dialogs.py", line 65, in __init__
pyfrp_gui_basics.listSelectorDialog.__init__(self,[],parent,leftTitle="Available Fits",rightTitle="Selected Fits")
File "/usr/local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_gui_basics.py", line 307, in __init__
super(listSelectorDialog,self).__init__(parent)
TypeError: QDialog(QWidget parent=None, Qt.WindowFlags flags=0): argument 1 has unexpected type 'list'
PyFRAP Wizard closes when in first geometry dialogue someone presses "Done", but continues when someone presses "X", reported under OSX.
In the first Dialog after embryo creation (setting basic image information such as resolution and imaging depth) the "preview" image is not shown.
Traceback (most recent call last):
File "/home/lin2-local/.local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_app.py", line 1235, in newEmbryo
self.editEmbryo()
File "/home/lin2-local/.local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_app.py", line 1285, in editEmbryo
ret=pyfrp_gui_embryo_dialogs.embryoDialog(currEmbryo,self).exec_()
File "/home/lin2-local/.local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_gui_embryo_dialogs.py", line 176, in init
self.showFirstDataImg()
File "/home/lin2-local/.local/lib/python2.7/site-packages/pyfrp/gui/pyfrp_gui_embryo_dialogs.py", line 277, in showFirstDataImg
img=pyfrp_img_module.loadImg(fnImg,self.embryo.dataEnc)
File "/home/lin2-local/.local/lib/python2.7/site-packages/pyfrp/modules/pyfrp_img_module.py", line 688, in loadImg
img = skimage.io.imread(fn).astype(enc)
File "/usr/lib/python2.7/dist-packages/skimage/io/_io.py", line 97, in imread
img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
File "/usr/lib/python2.7/dist-packages/skimage/io/manage_plugins.py", line 209, in call_plugin
return func(*args, **kwargs)
File "/usr/lib/python2.7/dist-packages/skimage/io/_plugins/pil_plugin.py", line 34, in imread
im = np.fromstring(im.tostring(), dtype)
File "/usr/lib/python2.7/dist-packages/PIL/Image.py", line 695, in tostring
"Please call tobytes() instead.")
Exception: tostring() has been removed. Please call tobytes() instead.
When calling
from pyfrp.modules import pyfrp_gmsh_IO_module
from pyfrp.modules import pyfrp_plot_module
import sys
sel=pyfrp_plot_module.FRAPBoundarySelector(fn=someImgFile)
c,r=sel.getResults()
d=pyfrp_gmsh_IO_module.readStlFile(someSTLfile)
d.draw(backend='vtk')
I get
Traceback (most recent call last):
File "readStl.py", line 8, in <module>
d=pyfrp_gmsh_IO_module.readStlFile(sys.argv[1])
File "/usr/local/lib/python2.7/dist-packages/pyfrp/modules/pyfrp_gmsh_IO_module.py", line 514, in readStlFile
mesh=meshstl.Mesh.from_file(fn)
File "/usr/local/lib/python2.7/dist-packages/stl/stl.py", line 316, in from_file
fh, mode=mode, speedups=speedups)
File "/usr/local/lib/python2.7/dist-packages/stl/stl.py", line 85, in load
name, data = cls._load_binary(fh, header, check_size=True)
File "/usr/local/lib/python2.7/dist-packages/stl/stl.py", line 102, in _load_binary
count, MAX_COUNT)
AssertionError: File too large, got 942551865 triangles which exceeds the maximum of 100000000
However, not calling the FRAPBoundarySelector
prevents the crash and everything is fine. globals()
and locals()
are not altered in any significant way.
PyFRAP reports "ERROR: Gmsh not working properly", even though Gmsh is working properly under OSX.
after installation Embryo creation failed with the error message:
sh: 1: /home/lin2-local/Software/PyFRAP/pyfrp/executables/Fiji.app/ImageJ-linux64: Permission denied
-> no execute rights for ImageJ-linux64
Gmsh seems to live in gmsh/gmsh.exe instead gmsh/bin/gmsh.exe .
The 3D Geometry on the right side of the Geometry is too small in Windows and IS NOT adjustable by increasing the size of the window:
Also, the window size in the ROI selection dialogs is a bit weird, because by default the lower panels are "squished". But this can be adjusted by changing the window size:
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