Merge pull request #12 from mvgorcum/pyinstall

mvgorcum · web-flow · commit 14231f971b54 · 2022-01-19T23:24:07.000+01:00
fix a bug when not detecting filetype, replace old qtgui objects
diff --git a/README.md b/README.md
@@ -19,7 +19,7 @@ A GUI using pyqtgraph and pyqt5 is available, as well as a standalone script. Th
 
 ## Prerequisites
 If you don't use the precomiled releases nor `pip install` it you'll need:
-The script requires numpy, pandas, scipy, pyqt5, opencv-python, scikit-image, imageio, shapely, pyqtgraph >=0.11.0, toml, h5py, json, and appdirs.
+The script requires numpy, pandas, scipy, pyqt5, opencv-python, fast-histogram, imageio, shapely, pyqtgraph >=0.11.0, openpyxl, toml, h5py, json, and appdirs.
 
 ## Install and running
 To install the program run `pip install .` in the sessile.drop.analysis folder.
diff --git a/README.md.backup b/README.md.backup
@@ -0,0 +1,44 @@
+# Python sessile drop analysis
+[![Element Android Matrix room #Sessile.Drop.Analysis:matrix.vgorcum.com](https://img.shields.io/matrix/Sessile.Drop.Analysis:matrix.vgorcum.com.svg?label=%23Sessile.Drop.Analysis:matrix.vgorcum.com&logo=matrix&server_fqdn=matrix.org)](https://matrix.to/#/#Sessile.Drop.Analysis:matrix.vgorcum.com)
+
+Made by Mathijs van Gorcum during his PhD at the Physics of Fluids group of the University of Twente.
+
+Python script to analyse sessile drops by measuring contact angle, drop volume and contact line speed.  
+This script analyses an image sequence (in the form of an avi, a tiffstack or a folder containing the images) and finds the contact angle, drop volume and the contact line speed.  
+The script assumes a black and white image of the drop on the surface, where the drop is black, and the background is white.  
+The script will ask for the file (or a file, in the case of a folder containing images), a crop (to increase calculation speed, and cut off any irrelevant parts) and a baseline.
+We use a subpixel edge detection, either fast, with a linear interpolation between two pixels around the edge, or slow by fitting an error function around the edge.
+To find the contact line position and the contact angle the detected edge is fitted with a 3rd order polynomial fit, and the slope of the baseline is also used to calculate the contact angles.
+Note that the drop volume assume cylindrical symmetry and if there is a needle present, the volume of the needle is added.
+
+A GUI using pyqtgraph and pyqt5 is available, as well as a standalone script. The old standalone script is probably beneficial when using an IDE like spyder and you want to be able to customize the inner workings of the script.
+
+## Screenshot
+
+![](Screenshot.png)
+
+## Prerequisites
+If you don't use the precomiled releases nor `pip install` it you'll need:
+The script requires numpy, pandas, scipy, pyqt5, opencv-python, fast_histogram, imageio, shapely, pyqtgraph >=0.11.0, openpyxl, toml, h5py, json, and appdirs.
+
+## Install and running
+To install the program run `pip install .` in the sessile.drop.analysis folder.
+To run the program after installing simply run `drop_analysis` in the terminal.
+
+To compile a binary, pyinstaller is required, use the following:
+`pyinstaller --name drop_analysis --additional-hooks-dir hooks --exclude-module matplotlib --icon drop_analysis/data/icon.ico --onefile pyinst_entrypoint.py`
+
+## Some details
+* The code is written for Python 3.8
+* The edge detection uses only a horizontal subpixel correction, and when fitting the errorfunction, 40 pixels left and right of the edge are used.  
+* To find the contact angle and contact point a polyfit is used, but the fit is made flipping the x and y coordinates, because polyfits don't perform well for vertical lines (ie at contact angles of 90 degrees).  
+* In the non-gui script, the variable k is used to set the amount of pixels used in the polyfit, by default set at 70.  
+* The thresh variable is the threshold level, for the fast edge detection the value is used explicitly while for the error function fitting the value is only used to find an approximate edge, to fit the errorfunction around.  
+* The contact line speed is calculated using a linear regression of the contact line position.  
+* The non-gui script calculates the speed in pixels/frame, and the volume in pixels^3, so be sure to convert it.
+
+## Contributing
+Feel free to send pull requests, critique my awful code or point out any issues.
+
+## License
+This project is licensed under the GPLv3 license - see the [LICENSE](https://github.com/mvgorcum/Sessile.drop.analysis/blob/master/LICENSE) file for details
diff --git a/drop_analysis/FrameSupply.py b/drop_analysis/FrameSupply.py
@@ -7,7 +7,7 @@
 import imageio
 import numpy as np
 from time import sleep
-from PyQt5 import QtGui
+from PyQt5 import QtGui, QtWidgets
 import datetime
 import h5py
 import json
@@ -256,9 +256,9 @@ def _aquire(self):
         firstrec=True
 
         if not self.cap.isOpened(): 
-            errorpopup=QtGui.QMessageBox()
+            errorpopup=QtWidgets.QMessageBox()
             errorpopup.setText('Error opening video stream')
-            errorpopup.setStandardButtons(QtGui.QMessageBox.Ok)
+            errorpopup.setStandardButtons(QtWidgets.QMessageBox.Ok)
             errorpopup.exec_()
             self.cap.release()
             self.is_running = False
diff --git a/drop_analysis/gui.py b/drop_analysis/gui.py
@@ -119,7 +119,12 @@ def openCall(self):
         mimetype=mimetypes.guess_type(VideoFile)[0]
         self.MeasurementResult=pd.DataFrame(columns=['thetaleft', 'thetaright', 'contactpointleft','contactpointright','volume','time'])
         self.PlotItem.clear()
-        if any(mimetype in key for key in filetypemap):
+        if mimetype is None or not any(mimetype in key for key in filetypemap):
+            errorpopup=QtWidgets.QMessageBox()
+            errorpopup.setText('Unkown filetype')
+            errorpopup.setStandardButtons(QtWidgets.QMessageBox.Ok)
+            errorpopup.exec_()
+        else:
             self.FrameSource=filetypemap[mimetype](VideoFile)
             self.FrameSource.start()
             FrameWidth,FrameHeight=self.FrameSource.getframesize()
@@ -128,11 +133,6 @@ def openCall(self):
             self.BaseLine.setPos([FrameWidth*.2,FrameHeight*.7])
             firstframe,_=self.FrameSource.getfirstframe()
             self.VideoItem.setImage(firstframe,autoRange=True)
-        else:
-            errorpopup=QtGui.QMessageBox()
-            errorpopup.setText('Unkown filetype')
-            errorpopup.setStandardButtons(QtGui.QMessageBox.Ok)
-            errorpopup.exec_()
 
 
     def StartStop(self):
@@ -256,9 +256,9 @@ def SaveResult(self):
 
             self.MaybeSave=False
         else:
-            errorpopup=QtGui.QMessageBox()
+            errorpopup=QtWidgets.QMessageBox()
             errorpopup.setText('Nothing to save')
-            errorpopup.setStandardButtons(QtGui.QMessageBox.Ok)
+            errorpopup.setStandardButtons(QtWidgets.QMessageBox.Ok)
             errorpopup.exec_()
 
     def configSettings(self):
@@ -274,14 +274,14 @@ def SaveVideo(self):
                     SaveFileName=SaveFileName+'.h5'
                 Path(self.FrameSource.bufferpath).rename(SaveFileName)
             else:
-                errorpopup=QtGui.QMessageBox()
+                errorpopup=QtWidgets.QMessageBox()
                 errorpopup.setText('No video has been recorded')
-                errorpopup.setStandardButtons(QtGui.QMessageBox.Ok)
+                errorpopup.setStandardButtons(QtWidgets.QMessageBox.Ok)
                 errorpopup.exec_()
         else:
-            errorpopup=QtGui.QMessageBox()
+            errorpopup=QtWidgets.QMessageBox()
             errorpopup.setText("Can't save video while recording is running")
-            errorpopup.setStandardButtons(QtGui.QMessageBox.Ok)
+            errorpopup.setStandardButtons(QtWidgets.QMessageBox.Ok)
             errorpopup.exec_()
 
     def ExportVideo(self):
@@ -290,9 +290,9 @@ def ExportVideo(self):
                 exportsource=FrameSupply.Hdf5Reader(self.FrameSource.bufferpath)
                 exportsource.start()
             elif self.CameraToggleButton.isChecked() or not Path(self.FrameSource.bufferpath).exists():
-                errorpopup=QtGui.QMessageBox()
+                errorpopup=QtWidgets.QMessageBox()
                 errorpopup.setText('No video has been recorded')
-                errorpopup.setStandardButtons(QtGui.QMessageBox.Ok)
+                errorpopup.setStandardButtons(QtWidgets.QMessageBox.Ok)
                 errorpopup.exec_()
             else:
                 exportsource=self.FrameSource
@@ -320,8 +320,8 @@ def ExportVideo(self):
             progress.setValue(totalframes)
             writer.release()
         else:
-            errorpopup=QtGui.QMessageBox()
+            errorpopup=QtWidgets.QMessageBox()
             errorpopup.setText("Can't export video while recording is running")
-            errorpopup.setStandardButtons(QtGui.QMessageBox.Ok)
+            errorpopup.setStandardButtons(QtWidgets.QMessageBox.Ok)
             errorpopup.exec_()
 
diff --git a/drop_analysis/settings.py b/drop_analysis/settings.py
@@ -58,9 +58,9 @@ def _tryframerate(self):
         try:
             cap = cv2.VideoCapture(0)
         except:
-            errorpopup=QtGui.QMessageBox()
+            errorpopup=QtWidgets.QMessageBox()
             errorpopup.setText('Error opening camera, is the Live Camera disabled?')
-            errorpopup.setStandardButtons(QtGui.QMessageBox.Ok)
+            errorpopup.setStandardButtons(QtWidgets.QMessageBox.Ok)
             errorpopup.exec_()
             return {}
         if cap.isOpened():
@@ -70,9 +70,9 @@ def _tryframerate(self):
             self.config['opencvcamera']['framerate']=actualframerate
 
         else:
-            errorpopup=QtGui.QMessageBox()
+            errorpopup=QtWidgets.QMessageBox()
             errorpopup.setText('Error opening camera, is the Live camera disabled?')
-            errorpopup.setStandardButtons(QtGui.QMessageBox.Ok)
+            errorpopup.setStandardButtons(QtWidgets.QMessageBox.Ok)
             errorpopup.exec_()
 
     def _saveconfig(self):
@@ -89,7 +89,7 @@ def _saveconfig(self):
             toml.dump(self.config,configfile)
 
     def _changebufferpath(self):
-        SaveFileName, _ =QtGui.QFileDialog.getSaveFileName(self,'Buffer file location', '', "Buffer file (*.h5)")
+        SaveFileName, _ =QtWidgets.QFileDialog.getSaveFileName(self,'Buffer file location', '', "Buffer file (*.h5)")
         if SaveFileName=='':
             return
         if Path(SaveFileName).suffix =='':
@@ -112,9 +112,9 @@ def detect_resolutions():
     try:
         cap = cv2.VideoCapture(0)
     except:
-        errorpopup=QtGui.QMessageBox()
+        errorpopup=QtWidgets.QMessageBox()
         errorpopup.setText('Error opening camera, is the Live Camera disabled?')
-        errorpopup.setStandardButtons(QtGui.QMessageBox.Ok)
+        errorpopup.setStandardButtons(QtWidgets.QMessageBox.Ok)
         errorpopup.exec_()
         return {}
     if cap.isOpened():
@@ -125,8 +125,8 @@ def detect_resolutions():
             height = int(cap.get(cv2.CAP_PROP_FRAME_HEIGHT))
             resolutions[str(width)+"x"+str(height)] = [width,height]
     else:
-        errorpopup=QtGui.QMessageBox()
+        errorpopup=QtWidgets.QMessageBox()
         errorpopup.setText('Error opening camera, is the Live camera disabled?')
-        errorpopup.setStandardButtons(QtGui.QMessageBox.Ok)
+        errorpopup.setStandardButtons(QtWidgets.QMessageBox.Ok)
         errorpopup.exec_()
     return resolutions
diff --git a/setup.cfg b/setup.cfg
@@ -20,7 +20,8 @@ install_requires =
   scipy
   pyqt5
   opencv-python-headless
-  scikit-image
+  openpyxl
+  fast-histogram
   imageio
   shapely
   pyqtgraph >=0.11.0
