Merge pull request #8 from nanthony21/dev

Dev

conda.recipe/meta.yaml

@@ -32,8 +32,8 @@ requirements:
     - google-auth-httplib2
     - google-auth-oauthlib
     - pyqt =5
-    - pwspy >=0.2.4 # Core pws package, available on backmanlab anaconda cloud account.
-    - mpl_qt_viz >=1.0.7  # Plotting package available on PyPi and the backmanlab anaconda cloud account. Written for this project by Nick Anthony
+    - pwspy >=0.2.8 # Core pws package, available on backmanlab anaconda cloud account.
+    - mpl_qt_viz >=1.0.9  # Plotting package available on PyPi and the backmanlab anaconda cloud account and conda-forge. Written for this project by Nick Anthony
     - descartes
     - cachetools >=4
 app:

setup.py

@@ -46,8 +46,8 @@
                         'google-auth-httplib2',
                         'google-auth-oauthlib',
                         'PyQt5',
-                        'pwspy>=0.2.4',  # Core pws package, available on backmanlab anaconda cloud account.
-                        'mpl_qt_viz>=1.0.7',  # Plotting package available on PyPi and the backmanlab anaconda cloud account. Written for this project by Nick Anthony
+                        'pwspy>=0.2.8',  # Core pws package, available on backmanlab anaconda cloud account.
+                        'mpl_qt_viz>=1.0.9',  # Plotting package available on PyPi and the backmanlab anaconda cloud account. Written for this project by Nick Anthony
                         'descartes',
                         'cachetools>=4'],
       package_dir={'': 'src'},

src/pwspy_gui/ExtraReflectanceCreator/ERWorkFlow.py

@@ -171,7 +171,7 @@ def deleteFigures(self):
     def loadCubes(self, includeSettings: t_.List[str], binning: int, parallelProcessing: bool):
         self.dataprovider.loadCubes(includeSettings, binning, parallelProcessing)
 
-    def plot(self, includeSettings: t_.List[str], binning: int, parallelProcessing: bool, numericalAperture: float, saveToPdf: bool = False, saveDir: str = None):
+    def plot(self, includeSettings: t_.List[str], binning: int, parallelProcessing: bool, numericalAperture: float):
         self.loadIfNeeded(includeSettings, binning, parallelProcessing)
         cubes = self.dataprovider.getCubes()
         materials = set(cubes['material'])
@@ -183,12 +183,6 @@ def plot(self, includeSettings: t_.List[str], binning: int, parallelProcessing:
         roi = cubes['cube'].sample(n=1).iloc[0].selectLassoROI()  # Select an ROI to analyze
         cubeDict = cubes.groupby('setting').apply(lambda df: df.groupby('material')['cube'].apply(list).to_dict()).to_dict()  # Transform data frame to a dict of dicts of lists for input to `plot`
         self.figs.extend(er.plotExtraReflection(cubeDict, theoryR, matCombos, numericalAperture, roi))
-        if saveToPdf:
-            with PdfPages(os.path.join(saveDir, f"fig_{datetime.strftime(datetime.now(), '%d-%m-%Y %HH%MM%SS')}.pdf")) as pp:
-                for i in plt.get_fignums():
-                    f = plt.figure(i)
-                    f.set_size_inches(9, 9)
-                    pp.savefig(f)
 
     def save(self, includeSettings: t_.List[str], binning: int, parallelProcessing: bool, numericalAperture: float, parentWidget: QWidget):
         self.loadIfNeeded(includeSettings, binning, parallelProcessing)
@@ -256,8 +250,7 @@ def compareDates(self, includeSettings: t_.List[str], binning: int, parallelProc
         anis = []
         figs = []  # These lists just maintain references to matplotlib figures to keep them responsive.
         cubes = self.dataprovider.getCubes()
-        verts = cubes['cube'].sample(n=1).iloc[0].selectLassoROI()  # Select a random of the selected cubes and use it to prompt the user for an analysis ROI
-        mask = Roi.fromVerts(verts=verts, dataShape=cubes['cube'].sample(n=1).iloc[0].data.shape[:-1])
+        roi = cubes['cube'].sample(n=1).iloc[0].selectLassoROI()  # Select a random of the selected cubes and use it to prompt the user for an analysis ROI
         for mat in set(cubes['material']):
             c = cubes[cubes['material'] == mat]
             fig, ax = plt.subplots()
@@ -270,7 +263,7 @@ def compareDates(self, includeSettings: t_.List[str], binning: int, parallelProc
             anims = []
             for i, row in c.iterrows():
                 im = row['cube']
-                spectra = im.getMeanSpectra(mask)[0]
+                spectra = im.getMeanSpectra(roi)[0]
                 ax.plot(im.wavelengths, spectra, label=row['setting'])
                 anims.append((ax2.imshow(im.data.mean(axis=2), animated=True,
                                          clim=[np.percentile(im.data, .5), np.percentile(im.data, 99.5)]),

src/pwspy_gui/ExtraReflectanceCreator/app.py

@@ -65,9 +65,7 @@ def connectWindowToWorkflow(self):
                     self.window.checkedSettings,
                     self.window.binning,
                     self.window.parallelProcessing,
-                    self.window.numericalAperture.value(),
-                    saveToPdf=True,
-                    saveDir=self.figsDir)))
+                    self.window.numericalAperture.value())))
 
     def checkDataDir(self):
         self.homeDir = os.path.join(appPath, 'ExtraReflectanceCreatorData')
@@ -76,9 +74,6 @@ def checkDataDir(self):
         self.gDriveDir = os.path.join(self.homeDir, 'GoogleDriveData')
         if not os.path.exists(self.gDriveDir):
             os.mkdir(self.gDriveDir)
-        self.figsDir = os.path.join(self.homeDir, 'Plots')
-        if not os.path.exists(self.figsDir):
-            os.mkdir(self.figsDir)
 
     def _cb(self, func):
         """Return a wrapped function with extra gui stuff."""

src/pwspy_gui/ExtraReflectanceCreator/examples/4waycalib.py

@@ -76,8 +76,8 @@ def processIm(im):
     theoryR = er.getTheoreticalReflectances(list(zip(*materials))[1], cubes['cube'][0].wavelengths, 0.52)
     matCombos = er.generateMaterialCombos(list(zip(*materials))[1], excludedCombos=exclude)
     if plotResults:
-        mask = random.choice(cubes['cube']).selectLassoRoi()
-        er.plotExtraReflection(cubes, theoryR, matCombos, 0.52, mask, plotReflectionImages=False)
+        roi = random.choice(cubes['cube']).selectLassoRoi()
+        er.plotExtraReflection(cubes, theoryR, matCombos, 0.52, roi, plotReflectionImages=False)
         with PdfPages(os.path.join(rootDir, "figs.pdf")) as pp:
             for i in plt.get_fignums():
                 f = plt.figure(i)

src/pwspy_gui/ExtraReflectanceCreator/examples/generateExtraReflectance.py

@@ -79,8 +79,7 @@ def processIm(im):
         theoryR = er.getTheoreticalReflectances(list(zip(*materials))[1], df['cube'][0].wavelengths, numericalAperture=na)
         matCombos = er.generateMaterialCombos(list(zip(*materials))[1])
         if plotResults:
-            verts = random.choice(df['cube']).selectLassoROI()
-            roi = Roi.fromVerts(verts, df['cube'][0].data.shape[:2])
+            roi = random.choice(df['cube']).selectLassoROI()
             er.plotExtraReflection(df, theoryR, matCombos, na, roi, plotReflectionImages=False)
             with PdfPages(os.path.join(rootDir, "figs.pdf")) as pp:
                 for i in plt.get_fignums():