Merge pull request #7 from gletort/bigfish_nan

add tophat as a parameter

Author: gletort

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "fishfeats"
-version = "1.4.4"
+version = "1.4.5"
 description = "Napari plugin for RNA-Fish+cells analysis pipeline"
 license.file = "LICENSE"
 readme = "README.md"

src/fish_feats/MainImage.py

@@ -772,25 +772,25 @@ def get_rna_threshold(self, rnachan):
             return self.rnas[rnachan].threshold
         return 0
 
-    def find_rna(self, rnachan, spotZRadius, spotXYRadius, rmExtremeZ, threshold=None):
+    def find_rna(self, rnachan, spotZRadius, spotXYRadius, rmExtremeZ, threshold=None, tophat_radius=0 ):
         if self.rnas.get(rnachan) is None:
             rnaspot = RNASpots(rnachan, verbose=self.verbose)
             self.rnas[rnachan] = rnaspot
         else:
             rnaspot = self.rnas[rnachan]
             rnaspot.reset_spots()
         rnaimg = self.image[rnachan,:,:,:]
-        rnaspot.detect_spots_withbigfish(rnaimg, scaleZ=self.scaleZ, scaleXY=self.scaleXY, spotZRadius=spotZRadius, spotXYRadius=spotXYRadius, rmextr=rmExtremeZ, threshold=threshold)
+        rnaspot.detect_spots_withbigfish(rnaimg, scaleZ=self.scaleZ, scaleXY=self.scaleXY, spotZRadius=spotZRadius, spotXYRadius=spotXYRadius, rmextr=rmExtremeZ, threshold=threshold, tophat_radius=tophat_radius )
 
-    def find_rnas_in_image(self, rnaimg, chanlist, spotZRadius, spotXYRadius, threshold=None):
+    def find_rnas_in_image(self, rnaimg, chanlist, spotZRadius, spotXYRadius, threshold=None, tophat_radius=0):
         chanlist = str(chanlist)
         if self.rnas.get(chanlist) is None:
             rnaspot = RNASpots(chanlist, verbose=self.verbose)
             self.rnas[chanlist] = rnaspot
         else:
             rnaspot = self.rnas[chanlist]
             rnaspot.reset_spots()
-        rnaspot.detect_spots_withbigfish(rnaimg, scaleZ=self.scaleZ, scaleXY=self.scaleXY, spotZRadius=spotZRadius, spotXYRadius=spotXYRadius, rmextr=False, threshold=threshold)
+        rnaspot.detect_spots_withbigfish(rnaimg, scaleZ=self.scaleZ, scaleXY=self.scaleXY, spotZRadius=spotZRadius, spotXYRadius=spotXYRadius, rmextr=False, threshold=threshold, tophat_radius=tophat_radius)
         return rnaspot.get_points()
 
     def find_blobs_in_image(self, rnaimg, chanlist, minSigma, threshold):

src/fish_feats/NapaRNA.py

@@ -50,6 +50,7 @@ def load_RNA_parameters(self, channel, paras):
         """ default or loaded RNA parameters """
         paras["RNA"+str(channel)+"_spotZRadiusNm"] = 1000
         paras["RNA"+str(channel)+"_spotXYRadiusNm"] = 250
+        paras["RNA"+str(channel)+"_tophatRadius"] = 20
         paras["RNA"+str(channel)+"_removeSpotInExtremeZ"] = True
         #paras["RNA"+str(channel)+"_drawing_spot_size"] = 3
         paras["RNA"+str(channel)+"_threshold"] = self.mig.get_rna_threshold(channel)
@@ -171,6 +172,11 @@ def __init__( self, napari_viewer, parameters, nchan, mig, cfg, defmethod, rnafi
         threshold_line.addWidget(self.automatic_threshold)
 
         bigfish_layout.addLayout(threshold_line)
+        
+        ## top-hat radius
+        tophat_line, self.tophat_radius = fwid.value_line( "TopHat radius (pixels)", 20, descr="Preprocessing with top-hat. Put 0 to disable" )
+        self.tophat_radius.setText( str(self.paras["RNA"+str(self.rnachannel)+"_tophatRadius"]) )
+        bigfish_layout.addLayout( tophat_line )
 
         self.remove_extrem = QCheckBox("Remove spots in extremes Z")
         self.remove_extrem.setChecked(False)
@@ -215,6 +221,7 @@ def go_rna(self):
         self.cfg.addParameter("RNA"+str(self.rnachannel), "RNA"+str(self.rnachannel)+"_method", self.method.currentText())
         self.cfg.addParameter( "RNA"+str(self.rnachannel), "RNA"+str(self.rnachannel)+"_spotZRadiusNm", int(self.spotz_radius.text()) )
         self.cfg.addParameter( "RNA"+str(self.rnachannel), "RNA"+str(self.rnachannel)+"_spotXYRadiusNm", int(self.spotxy_radius.text()) )
+        self.cfg.addParameter( "RNA"+str(self.rnachannel), "RNA"+str(self.rnachannel)+"_tophatRadius", int(self.tophat_radius.text()) )
         self.cfg.addParameter( "RNA"+str(self.rnachannel), "RNA"+str(self.rnachannel)+"_threshold", float(self.threshold.text()) )
         self.cfg.addParameter( "RNA"+str(self.rnachannel), "RNA"+str(self.rnachannel)+"_removeSpotInExtremeZ", self.remove_extrem.isChecked() )
         #cfg.addParameter( "RNA"+str(rna_channel), "RNA"+str(rna_channel)+"_drawing_spot_size", drawing_spot_size )
@@ -274,6 +281,7 @@ def channel_choice(self):
         self.filename.setText(rnafilename)
         self.spotz_radius.setText(str(self.paras["RNA"+str(self.rnachannel)+"_spotZRadiusNm"]))
         self.spotxy_radius.setText(str(self.paras["RNA"+str(self.rnachannel)+"_spotXYRadiusNm"]))
+        self.tophat_radius.setText(str(self.paras["RNA"+str(self.rnachannel)+"_tophatRadius"]))
         self.threshold.setText(str(self.paras["RNA"+str(self.rnachannel)+"_threshold"]))
         self.automatic_threshold.setChecked( self.paras["RNA"+str(self.rnachannel)+"_automatic_threshold"] )
         self.remove_extrem.setChecked( self.paras["RNA"+str(self.rnachannel)+"_removeSpotInExtremeZ"] )
@@ -291,9 +299,10 @@ def load_segmentationfile_rna(self ):
         self.end_segmented_rna()
 
     def segment_rna(self, threshold):
+        """ Launch the segmentation with selected parameters """
         chanel = self.rnachannel
         start_time = time.time()
-        self.mig.find_rna( self.rnachannel, int(self.spotz_radius.text()), int(self.spotxy_radius.text()), self.remove_extrem.isChecked(), threshold )
+        self.mig.find_rna( self.rnachannel, int(self.spotz_radius.text()), int(self.spotxy_radius.text()), self.remove_extrem.isChecked(), threshold, int(self.tophat_radius.text()) )
         print("RNA big-fish segmentation finished in {:.3f}".format((time.time()-start_time)/60)+" min")
         self.end_segmented_rna()
 

src/fish_feats/RNASpots.py

@@ -50,11 +50,12 @@ def nspots(self):
             return len(self.spots)
         return 0
 
-    def detect_spots_withbigfish(self, img, scaleZ, scaleXY, spotZRadius, spotXYRadius, rmextr=True, threshold=None):
+    def detect_spots_withbigfish(self, img, scaleZ, scaleXY, spotZRadius, spotXYRadius, rmextr=True, threshold=None, tophat_radius=0):
         """ Detect RNA spots with big-fish """
-        from fish_feats.Separe import topHat
         from fish_feats.SegmentObj import normalizeQuantile
-        img = topHat(img, xyrad=floor(30*scaleXY))
+        if tophat_radius > 0:
+            from fish_feats.Separe import topHat
+            img = topHat( img, xyrad=floor(tophat_radius) )
         img = normalizeQuantile(img, qmin=0.001, qmax=0.999, vmax=255)
         # detect with big-Fish: spots sizes are to be put in nanometers
         spots, self.threshold = detection.detect_spots(