alexblaessle · alexblaessle · Oct 16, 2019 · Nov 5, 2019 · Nov 5, 2019 · Nov 5, 2019
diff --git a/.cache/v/cache/lastfailed b/.cache/v/cache/lastfailed
diff --git a/.directory b/.directory
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 # Don't push data
 Benchmarking/
 TestDataset/
+packages/
 
 # Don't push older versions
 oldversions/
@@ -71,7 +72,7 @@ PyFRAP.wiki/
 
 # Don't push .zip files
 *zip
-
+*.bak
 
 
 

diff --git a/2to3_folder.py b/2to3_folder.py
@@ -0,0 +1,15 @@
+import os
+import glob
+import sys
+
+files=glob.glob(sys.argv[1]+'*.py')
+
+for i,f in enumerate(files):
+
+	print("%i/%i: Fixing %s"%(i,len(files),f))
+
+	cmd="2to3 -w %s"%f
+	os.system(cmd)
+
+
+
diff --git a/ChangeLog.txt b/ChangeLog.txt
diff --git a/LICENSE b/LICENSE
diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/PyFRAP.wiki_backup b/PyFRAP.wiki_backup
diff --git a/README.md b/README.md
diff --git a/_config.yml b/_config.yml
diff --git a/build_app.py b/build_app.py
@@ -0,0 +1,22 @@
+import os
+import sys
+import platform
+
+print("This system is running", platform.system(), platform.release(), platform.architecture()[0])
+arch1=platform.architecture()[0]
+arch2=platform.machine()
+
+if platform.system() in ["Darwin"]:
+	name="pyfrap_"+"OSX_"+platform.mac_ver()[0]+"_"+arch1
+	os.system("pyinstaller -F -y -n "+ name +" -i logo/pyfdap_icon.icns --windowed pyfdap_app.py")
+elif platform.system() in ["Linux"]:
+	name="pyfrap_"+"Linux_"+platform.release()+"_"+arch1
+	#os.system("pyinstaller -F -y -n "+ name +" -i logo/pyfdap_icon.ico --windowed pyfdap_app.py")
+	os.system("pyinstaller -F -y -n "+ name +" --windowed "+sys.argv[1])
+elif platform.system() in ["Windows"]:
+	name="pyfdap_"+"Win_"+platform.release()+"_"+arch1
+	if arch1=="64bit":
+		os.system("pyinstaller -F -y -i logo/pyfdap_icon.ico -n" + name +" pyfdap_app.py")
+	else:
+		os.system("pyinstaller -F -y -i logo/pyfdap_icon.ico -n" + name +" pyfdap_app_win32build.py")
+
diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/imgs/pyfrp_ROI/plotSimConcProfile.png b/docs/imgs/pyfrp_ROI/plotSimConcProfile.png
diff --git a/docs/imgs/pyfrp_fit/fit.png b/docs/imgs/pyfrp_fit/fit.png
diff --git a/docs/imgs/pyfrp_geometry/ball.eps b/docs/imgs/pyfrp_geometry/ball.eps
diff --git a/docs/imgs/pyfrp_geometry/ball.png b/docs/imgs/pyfrp_geometry/ball.png
diff --git a/docs/imgs/pyfrp_geometry/boundaryLayerField_geometry.png b/docs/imgs/pyfrp_geometry/boundaryLayerField_geometry.png
diff --git a/docs/imgs/pyfrp_geometry/boundaryLayerField_mesh.png b/docs/imgs/pyfrp_geometry/boundaryLayerField_mesh.png
diff --git a/docs/imgs/pyfrp_geometry/cone.eps b/docs/imgs/pyfrp_geometry/cone.eps
diff --git a/docs/imgs/pyfrp_geometry/cone.png b/docs/imgs/pyfrp_geometry/cone.png
diff --git a/docs/imgs/pyfrp_geometry/cylinder.eps b/docs/imgs/pyfrp_geometry/cylinder.eps
diff --git a/docs/imgs/pyfrp_geometry/cylinder.png b/docs/imgs/pyfrp_geometry/cylinder.png
diff --git a/docs/imgs/pyfrp_geometry/cylinderquad.eps b/docs/imgs/pyfrp_geometry/cylinderquad.eps
diff --git a/docs/imgs/pyfrp_geometry/cylinderquad.png b/docs/imgs/pyfrp_geometry/cylinderquad.png
diff --git a/docs/imgs/pyfrp_geometry/dome.eps b/docs/imgs/pyfrp_geometry/dome.eps
diff --git a/docs/imgs/pyfrp_geometry/dome.png b/docs/imgs/pyfrp_geometry/dome.png
diff --git a/docs/imgs/pyfrp_geometry/domequad.eps b/docs/imgs/pyfrp_geometry/domequad.eps
diff --git a/docs/imgs/pyfrp_geometry/domequad.png b/docs/imgs/pyfrp_geometry/domequad.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/addBallByParameters.png b/docs/imgs/pyfrp_gmsh_geometry/addBallByParameters.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/addCircleByParameters.png b/docs/imgs/pyfrp_gmsh_geometry/addCircleByParameters.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/addCuboidByParameters.png b/docs/imgs/pyfrp_gmsh_geometry/addCuboidByParameters.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/addCylinderByParameters.png b/docs/imgs/pyfrp_gmsh_geometry/addCylinderByParameters.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/addPolygonByParameters.png b/docs/imgs/pyfrp_gmsh_geometry/addPolygonByParameters.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/addPrismByParameters.png b/docs/imgs/pyfrp_gmsh_geometry/addPrismByParameters.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/addRectangleByParameters.png b/docs/imgs/pyfrp_gmsh_geometry/addRectangleByParameters.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/addSquareByParameters.png b/docs/imgs/pyfrp_gmsh_geometry/addSquareByParameters.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/approxBySpline1.png b/docs/imgs/pyfrp_gmsh_geometry/approxBySpline1.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/approxBySpline2.png b/docs/imgs/pyfrp_gmsh_geometry/approxBySpline2.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/arc.png b/docs/imgs/pyfrp_gmsh_geometry/arc.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/arc.svg b/docs/imgs/pyfrp_gmsh_geometry/arc.svg
diff --git a/docs/imgs/pyfrp_gmsh_geometry/boundaryLayerField_geometry.png b/docs/imgs/pyfrp_gmsh_geometry/boundaryLayerField_geometry.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/boundaryLayerField_mesh.png b/docs/imgs/pyfrp_gmsh_geometry/boundaryLayerField_mesh.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/thresholdField.png b/docs/imgs/pyfrp_gmsh_geometry/thresholdField.png
diff --git a/docs/imgs/pyfrp_gmsh_geometry/thresholdField.svg b/docs/imgs/pyfrp_gmsh_geometry/thresholdField.svg
diff --git a/docs/imgs/pyfrp_gui_vtk/vtkSimVisualizer.png b/docs/imgs/pyfrp_gui_vtk/vtkSimVisualizer.png
diff --git a/docs/imgs/pyfrp_gui_vtk/vtkSimVisualizerCutter.png b/docs/imgs/pyfrp_gui_vtk/vtkSimVisualizerCutter.png
diff --git a/docs/imgs/pyfrp_idx_module/neighbours3D.png b/docs/imgs/pyfrp_idx_module/neighbours3D.png
diff --git a/docs/imgs/pyfrp_img_module/genFakeIC.png b/docs/imgs/pyfrp_img_module/genFakeIC.png
diff --git a/docs/imgs/pyfrp_img_module/genFakeSigmoidIC.png b/docs/imgs/pyfrp_img_module/genFakeSigmoidIC.png
diff --git a/docs/imgs/pyfrp_img_module/plotRadialHist.png b/docs/imgs/pyfrp_img_module/plotRadialHist.png
diff --git a/docs/imgs/pyfrp_img_module/plotRadialProfile.png b/docs/imgs/pyfrp_img_module/plotRadialProfile.png
diff --git a/docs/imgs/pyfrp_mesh/density_plot.png b/docs/imgs/pyfrp_mesh/density_plot.png
diff --git a/docs/imgs/pyfrp_mesh/plotCellCenters.png b/docs/imgs/pyfrp_mesh/plotCellCenters.png
diff --git a/docs/imgs/pyfrp_plot_module/makeSubplot.png b/docs/imgs/pyfrp_plot_module/makeSubplot.png
diff --git a/docs/imgs/pyfrp_sim_module/sigmoidFct.png b/docs/imgs/pyfrp_sim_module/sigmoidFct.png
diff --git a/docs/imgs/pyfrp_simulation/ICcompare.png b/docs/imgs/pyfrp_simulation/ICcompare.png
diff --git a/docs/imgs/pyfrp_simulation/ICstack.png b/docs/imgs/pyfrp_simulation/ICstack.png
diff --git a/docs/imgs/pyfrp_simulation/showIC.png b/docs/imgs/pyfrp_simulation/showIC.png
diff --git a/docs/imgs/pyfrp_simulation/showICimg.png b/docs/imgs/pyfrp_simulation/showICimg.png
diff --git a/docs/imgs/pyfrp_simulation/showInterpolatedIC.png b/docs/imgs/pyfrp_simulation/showInterpolatedIC.png
diff --git a/docs/imgs/pyfrp_simulation/showInterpolatedICimg.png b/docs/imgs/pyfrp_simulation/showInterpolatedICimg.png
diff --git a/docs/make.bat b/docs/make.bat
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -57,13 +57,13 @@
 			'scipy','scipy.optimize','scipy.interpolate','scipy.ndimage','scipy.ndimage.interpolation',
 			#Matplotlib (and all submodules)
 			'matplotlib', 'matplotlib.pyplot','matplotlib.axes','mpl_toolkits','mpl_toolkits.mplot3d','matplotlib.collections',
-			'matplotlib.patches','matplotlib.tri','matplotlib.backends','matplotlib.backends.backend_qt4agg',
-			'matplotlib.bakends.backend_qt4agg.FigureCanvasQTAgg','matplotlib.backends.backend_qt4agg.FigureCanvas',
+			'matplotlib.patches','matplotlib.tri','matplotlib.backends','matplotlib.backends.backend_qt5agg',
+			'matplotlib.bakends.backend_qt5agg.FigureCanvasQTAgg','matplotlib.backends.backend_qt5agg.FigureCanvas',
 			'matplotlib.figure','mpl_toolkits.mplot3d.art3d',
 			#Skimage 
 			'skimage','skimage.io','skimage.morphology','scipy.signal','skimage.measure','skimage.filters',
 			#PyQT
-			'PyQt4','PyQt4.QtGui','PyQt4.QtCore',
+			'PyQt5','PyQt5.QtGui','PyQt5.QtCore',
 			#MeshIO
 			'meshio',
 			#VTK

diff --git a/docs/source/index.rst b/docs/source/index.rst
diff --git a/docs/source/modules.rst b/docs/source/modules.rst
diff --git a/docs/source/pyfrp.gui.rst b/docs/source/pyfrp.gui.rst
diff --git a/docs/source/pyfrp.modules.rst b/docs/source/pyfrp.modules.rst
diff --git a/docs/source/pyfrp.rst b/docs/source/pyfrp.rst
diff --git a/docs/source/pyfrp.subclasses.rst b/docs/source/pyfrp.subclasses.rst
diff --git a/docs/source/setup.rst b/docs/source/setup.rst
diff --git a/examples/geometryAndMeshing/attractorMesh.py b/examples/geometryAndMeshing/attractorMesh.py
diff --git a/examples/geometryAndMeshing/bleachedBL.py b/examples/geometryAndMeshing/bleachedBL.py
diff --git a/examples/geometryAndMeshing/createCircularGeometry.py b/examples/geometryAndMeshing/createCircularGeometry.py
diff --git a/examples/geometryAndMeshing/createCylinderGeometry.py b/examples/geometryAndMeshing/createCylinderGeometry.py
diff --git a/examples/geometryAndMeshing/mergedROIMesh.py b/examples/geometryAndMeshing/mergedROIMesh.py
diff --git a/examples/geometryAndMeshing/sliceBL.py b/examples/geometryAndMeshing/sliceBL.py
diff --git a/examples/geometryAndMeshing/test.eps b/examples/geometryAndMeshing/test.eps
diff --git a/examples/scripting/demo.geo b/examples/scripting/demo.geo
diff --git a/examples/scripting/simpleAnalysis.py b/examples/scripting/simpleAnalysis.py
@@ -104,11 +104,11 @@
 stopTime=time.time()
 
 # Print time it took
-print "Analysis done in ", stopTime-starTime , " seconds."
+print("Analysis done in ", stopTime-starTime , " seconds.")
 
 try:
 	emb.save(sys.argv[2])
 except IndexError:
-	print "Did not save embryo, no output given."	
+	print("Did not save embryo, no output given.")
 
-raw_input()
+input()
diff --git a/examples/visualization/visualizeMesh.py b/examples/visualization/visualizeMesh.py
diff --git a/examples/visualization/visualizeSimulation.py b/examples/visualization/visualizeSimulation.py
diff --git a/install_linux.sh b/install_linux.sh
@@ -4,26 +4,26 @@
 sudo apt-get install -y git
 sudo apt-get install default-jdk
 sudo apt-get install default-jre
-sudo apt-get install -y python-numpy
-sudo apt-get install -y python-scipy
-sudo apt-get install -y python-matplotlib
-sudo apt-get install -y python-qt4
-sudo apt-get install -y python-skimage
-sudo apt-get install -y python-vtk
+sudo apt-get install -y python3-numpy
+sudo apt-get install -y python3-scipy
+sudo apt-get install -y python3-matplotlib
+sudo apt-get install -y python3-pyqt5
+sudo apt-get install -y python3-skimage
+sudo apt-get install -y python3-vtk
 
 # Install everything that is in pip
-sudo pip install fipy
-sudo pip install solidpython
-sudo pip install numpy-stl
-sudo pip install wget
-sudo pip install python-bioformats
+sudo pip3 install fipy
+sudo pip3 install solidpython
+sudo pip3 install numpy-stl
+sudo pip3 install wget
+sudo pip3 install python-bioformats
 
 # Install openscad
 sudo apt-get install openscad
 
 # Clone PyFRAP and install
-cd PyFRAP-master
-sudo python setup.py install
+# cd PyFRAP-master
+# sudo python setup.py install
 
 
 

diff --git a/install_linux_new.sh b/install_linux_new.sh
diff --git a/install_win.bat b/install_win.bat
diff --git a/notebooks/.ipynb_checkpoints/Untitled-checkpoint.ipynb b/notebooks/.ipynb_checkpoints/Untitled-checkpoint.ipynb
@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/notebooks/.ipynb_checkpoints/analyse_embryo-checkpoint.ipynb b/notebooks/.ipynb_checkpoints/analyse_embryo-checkpoint.ipynb
@@ -0,0 +1,66 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[33mWARNING (<module>): \u001b[39mCannot import bioformats\n"
+     ]
+    },
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'vtk'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-1-93acdc2ba790>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;32m~/anaconda3/lib/python3.7/site-packages/pyfrp/__init__.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     19\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     20\u001b[0m \u001b[0;31m#Basic PyFRAP modules\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 21\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mmodules\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     22\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     23\u001b[0m \u001b[0;31m#PyFRAP classes\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/anaconda3/lib/python3.7/site-packages/pyfrp/modules/__init__.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     20\u001b[0m \u001b[0;31m#Basic PyFRAP modules\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     21\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp_term_module\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 22\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp_IO_module\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     23\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp_misc_module\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     24\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp_plot_module\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/anaconda3/lib/python3.7/site-packages/pyfrp/modules/pyfrp_IO_module.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     43\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     44\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mpyfrp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp_misc_module\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 45\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mpyfrp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp_gmsh_IO_module\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     46\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mpyfrp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpyfrp_term_module\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     47\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/anaconda3/lib/python3.7/site-packages/pyfrp/modules/pyfrp_gmsh_IO_module.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     47\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     48\u001b[0m \u001b[0;31m#PyFRAP Modules\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 49\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp_gmsh_geometry\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     50\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp_misc_module\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     51\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp_gmsh_module\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/anaconda3/lib/python3.7/site-packages/pyfrp/modules/pyfrp_gmsh_geometry.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     64\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp_geometry_module\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     65\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp_IO_module\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 66\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyfrp_vtk_module\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     67\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     68\u001b[0m \u001b[0;31m#Matplotlib\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/anaconda3/lib/python3.7/site-packages/pyfrp/modules/pyfrp_vtk_module.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     41\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     42\u001b[0m \u001b[0;31m#Plotting\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 43\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mvtk\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     44\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mmatplotlib\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     45\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'vtk'"
+     ]
+    }
+   ],
+   "source": [
+    "import pyfrp"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/notebooks/Untitled.ipynb b/notebooks/Untitled.ipynb
@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/notebooks/analyse_embryo.ipynb b/notebooks/analyse_embryo.ipynb
@@ -0,0 +1,58 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import sys\n",
+    "\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "import pyfrp"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "in_dir='../TestDataset/embryo/sqtGFP_20170609_01/recover/'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "nation"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/pyfdap_Linux_5.0.0-29-generic_64bit.spec b/pyfdap_Linux_5.0.0-29-generic_64bit.spec
@@ -0,0 +1,33 @@
+# -*- mode: python ; coding: utf-8 -*-
+
+block_cipher = None
+
+
+a = Analysis(['pyfrp/PyFRAP.py'],
+             pathex=['/home/alexander/Dropbox/Alex/Documents/Research/PyFRAP'],
+             binaries=[],
+             datas=[],
+             hiddenimports=[],
+             hookspath=[],
+             runtime_hooks=[],
+             excludes=[],
+             win_no_prefer_redirects=False,
+             win_private_assemblies=False,
+             cipher=block_cipher,
+             noarchive=False)
+pyz = PYZ(a.pure, a.zipped_data,
+             cipher=block_cipher)
+exe = EXE(pyz,
+          a.scripts,
+          a.binaries,
+          a.zipfiles,
+          a.datas,
+          [],
+          name='pyfdap_Linux_5.0.0-29-generic_64bit',
+          debug=False,
+          bootloader_ignore_signals=False,
+          strip=False,
+          upx=True,
+          upx_exclude=[],
+          runtime_tmpdir=None,
+          console=False )