Merge pull request #14 from fgjorup/JOSS-submission

Joss submission

.github/workflows/draft-pdf.yml

@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper.pdf

README.md

@@ -2,8 +2,6 @@
 Tool for visualizing Rietveld refinement results
 By Frederik Gjørup
 
-The software provided here is intended only for internal use at Department of Chemistry, Aarhus University, and should not be distributed outside of the institute without the consent of the author.  
-
 ### Running the program ###
 Please run the setup.bat the first time you use the program. After that, run it by running the "run_Reel.bat" file or double-clicking the corresponding short-cut.  
 If the program does not open, check that the path to python.exe in "run_Reel.bat" line 5 is valid.
@@ -26,12 +24,17 @@ Open a terminal in the program folder and run "Refinement_evaluator_ver1.0.py" i
 ### Requirements ###
 Python 3.8.3 (Other versions of python 3 and modules might still work)  
 Non-built-in python modules:  
-Module | Version | pip install command
------- | ------- | -------------------
-PyQt5 | v. 5.14.2 | pip install PyQt5
-pyqtgraph | v. 0.11.1 | pip install pyqtgraph
-matplotlib | v. 3.3.3 | pip install matplotlib
-numpy | v. 1.19.5 | pip install numpy
-scipy | v. 1.6.0 | pip install scipy
+| Module | Version | pip install command |
+| ------ | ------- | ------------------- |
+| PyQt5 | v. 5.14.2 | pip install PyQt5 |
+| pyqtgraph | v. 0.11.1 | pip install pyqtgraph |
+| matplotlib | v. 3.3.3 | pip install matplotlib |
+| numpy | v. 1.19.5 | pip install numpy |
+| scipy | v. 1.6.0 | pip install scipy |
 
 \+ Requirements imposed by the modules. See `pip show [module]` for more information.
+
+### Contributing, feedback, and support ###
+You can open a series of test files intended for debugging by running `Refinement_evaluator_ver1.0.py -debug`. 
+
+All users are welcome to provide feedback, report issues, or suggest changes to the program, either by creating a new issue on the GitHub [repository](https://github.com/fgjorup/Reel) or by contacting me at <fgjorup@chem.au.dk>.  

Reel1.0/Refinement_evaluator_ver1.0.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 """
-Last update: 22/06/2021
+Last update: 27/08/2021
 Frederik H. Gjørup
 """
 
@@ -106,7 +106,19 @@ def __init__(self):
         self.scale_surf = us.default_surface_scale
         self.scale_pat = us.default_pattern_scale
         self.initScale()
-
+
+        if '-debug' in sys.argv:
+            self.openTestfiles()
+
+    def openTestfiles(self):
+        path = os.path.abspath('_test_files')
+        test_sets = os.listdir(path)
+        for tset in test_sets:
+            ts_path = os.path.join(path,tset)
+            files = [os.path.join(ts_path,f) for f in os.listdir(ts_path) if f.endswith(tset)]
+            ext = '*.'+files[0].split('.')[-1]
+            self.addDataset(self,files=files,ext=ext)
+
     def keyPressEvent(self,event):
         if event.modifiers() == Qt.ControlModifier:
             if event.key() == Qt.Key_Left:
@@ -199,7 +211,7 @@ def changeDataset(self,index):
         self.parw.updateVline(im.shape[2]-h_pos+0.5)
         self.showCurrentWavelength()
 
-    def addDataset(self,is_par=False):
+    def addDataset(self,is_par=False,files=None,ext=None):
         self.im.append(np.zeros((3,100,100)))
         self.tth.append(np.arange(0,100,1))
         self.files.append([''])
@@ -211,7 +223,7 @@ def addDataset(self,is_par=False):
         self.datasets.append('')
         self.dataset_index = len(self.im)-1
         if is_par != True:
-            self.openFiles()
+            self.openFiles(files,ext)
 
     def removeDataset(self):
         if len(self.im)==1:
@@ -249,7 +261,8 @@ def removeAllDatasets(self):
 
     def plotLogo(self):
         self.scale_surf, self.scale_pat = ['linear']*2
-        self.openFiles(files=['_lib\icons\Main.raw'],ext='*.raw')
+        fname = os.path.abspath('_lib/icons/Main.raw')
+        self.openFiles(files=[fname],ext='*.raw')
         # im = self.im[0][0]
         # x = np.arange(0,im.shape[0],1)
         # y = np.flip(np.nanmean(im,axis=0))
@@ -737,10 +750,10 @@ def openFiles(self,files=None,ext=None):
         if not isinstance(files,list):
             path = self.path
             if not path:
-                path = os.environ['USERPROFILE']
+                path = os.getenv('USERPROFILE','')
             if ext != '*.csv':
                 ext = us.default_file_extension
-            filters = '*.xyy;;*.prf;;*.par;;*.dat;;*.xye *.xy;;*.csv'    
+            filters = '*.xyy;;*.prf;;*.dat;;*.xye *.xy;;*.csv'    
             filters = ext+';;'+';;'.join([x for x in filters.replace(ext,'').split(';;') if x])
             files, ext =  QtWidgets.QFileDialog.getOpenFileNames(self, 'Select files', path , filters)
         if len(files)<1:
@@ -759,7 +772,7 @@ def openFiles(self,files=None,ext=None):
                     im, tth, files, lambd, param, sub_plots, bgr, par_file, was_canceled = self.openPRF(files)
                 elif ext=='*.dat':
                     im, tth, files, lambd, param, sub_plots, bgr, par_file, was_canceled = self.openDAT(files)
-                elif ext=='*.xye *.xy':
+                elif ext=='*.xye *.xy' or ext=='*.xye' or ext=='*.xy':
                     im, tth, files, lambd, param, sub_plots, bgr, par_file, was_canceled = self.openXYE(files)
                 elif ext=='*.csv':
                     im, tth, files, lambd, param, sub_plots, bgr, par_file, was_canceled = self.openCSV(files[0])

Reel1.0/Setup.bat

@@ -5,7 +5,7 @@ ECHO CD %~dp0 >> Run_Reel.bat
 ECHO ECHO Opening Reel 1.0... >> Run_Reel.bat
 FOR %%i IN (python.exe) DO (
     IF EXIST "%%~$PATH:i" (
-       ECHO %%~$PATH:i Refinement_evaluator_ver1.0.py >> Run_Reel.bat
+       ECHO "%%~$PATH:i" Refinement_evaluator_ver1.0.py >> Run_Reel.bat
     ) ELSE (
         ECHO python.exe Refinement_evaluator_ver1.0.py >> Run_Reel.bat
         ECHO ATTENTION!

Reel1.0/_lib/ReelPlotWidgets.py

@@ -1,8 +1,9 @@
 # -*- coding: utf-8 -*-
 """
-Last update: 07/06/2021
+Last update: 27/08/2021
 Frederik H. Gjørup
 """
+import os
 try:
     from PyQt5 import QtCore
     import pyqtgraph as pg
@@ -28,8 +29,8 @@ def convertColormapMPtoPG(cmap):
 
 class MultiImageWidget(pg.GraphicsLayoutWidget):
 
-    sigHLineDragged = QtCore.Signal(object)
-    sigVLineDragged = QtCore.Signal(object)
+    sigHLineDragged = QtCore.pyqtSignal(object)
+    sigVLineDragged = QtCore.pyqtSignal(object)
 
     def __init__(self,n_images=1,labels=()):
         pg.GraphicsLayoutWidget.__init__(self)
@@ -65,8 +66,8 @@ def __init__(self,n_images=1,labels=()):
                         minXRange=10, 
                         yMin=-5,
                         minYRange=10)
-
-            im = np.fromfile('_lib\icons\Main.raw', dtype='ubyte').reshape(230,230).astype(float)
+            fname = os.path.abspath('_lib/icons/Main.raw')
+            im = np.fromfile(fname, dtype='ubyte').reshape(230,230).astype(float)
             im = np.abs(im-im.max())
             data = np.flipud(np.rot90(im))
             if i<2:
@@ -330,7 +331,7 @@ def setResData(self,x,y):
 
 class PlotParametersWidget(pg.PlotWidget):
 
-    sigVLineDragged = QtCore.Signal(object)
+    sigVLineDragged = QtCore.pyqtSignal(object)
 
     def __init__(self):
         pg.PlotWidget.__init__(self)