export ok, background correction started

volker/toolsets/measure_intensity_without_spots/conversion.py

@@ -0,0 +1,81 @@
+import os
+from ij import ImagePlus
+from ij import ImageStack 
+from ij.io import FileSaver
+from ij.plugin import RGBStackMerge
+from loci.plugins import BF
+from loci.plugins.in import ImporterOptions
+from loci.formats import ImageReader
+
+
+class BFWellsSeriesToTifStackSeries(object):
+
+
+    def __init__(self, path):
+        self.inputPath = path
+        self.outputFolderName = "export"
+
+
+    def setOutputFolderName(self, name):
+        self.outputFolderName = name
+
+
+    def getOutputPath(self):
+         outputPath = os.path.join(os.path.dirname(self.inputPath), self.outputFolderName)
+         if not os.path.exists(outputPath):
+            os.makedirs(outputPath)
+         return outputPath
+
+
+    def getNumberOfChannels(self):        
+        reader = ImageReader()
+        reader.setId(self.inputPath)
+        nrOfChannels = reader.getSizeC()
+        return nrOfChannels
+
+
+    def getOptions(self):
+        options = ImporterOptions()
+        options.setId(self.inputPath)
+        options.setOpenAllSeries(True)
+        options.setSplitChannels(True)
+        return options
+
+
+    def getImages(self):
+        images = list(BF.openImagePlus(self.getOptions()))
+        width = images[0].getWidth()
+        height = images[0].getHeight()
+        return images, width, height
+
+
+    def run(self):
+        nrOfChannels = self.getNumberOfChannels()
+        options = self.getOptions()
+        images, width, height = self.getImages()
+        cStacks = [None]*nrOfChannels
+        for c in range(nrOfChannels):
+            cStacks[c] = ImageStack(width, height)
+        lastWell = None
+        title = ""
+        cImages = [None]*nrOfChannels
+        for c in range(nrOfChannels):
+            cImages[c] = [image for i, image in enumerate(images) if i%2==c]
+        for cImageTupel in zip(*cImages):
+            title = cImageTupel[0].getTitle()
+            calibration = cImageTupel[0].getCalibration()
+            well = title.split("Well ")[1].split(" Field")[0]
+            if well == lastWell or lastWell==None: 
+                for c in range(nrOfChannels):
+                    cStacks[c].addSlice(cImageTupel[c].getProcessor())             
+            else:
+                imagesC = [ImagePlus(title.replace("C=0", "C=" + str(c)), cStacks[c]) for c in range(nrOfChannels)]
+                resultImage = RGBStackMerge.mergeChannels(imagesC, False)
+                resultImage.setCalibration(calibration)
+                saver = FileSaver(resultImage)
+                print(os.path.join(self.getOutputPath(), title.replace(" - C=0", "")))
+                saver.saveAsTiffStack(os.path.join(self.getOutputPath(), title.replace(" - C=0", "")))
+                cStacks = [None]*nrOfChannels
+                for c in range(nrOfChannels):
+                    cStacks[c] = ImageStack(width, height)
+            lastWell = well

volker/toolsets/measure_intensity_without_spots/correct_background.py

@@ -0,0 +1,11 @@
+from ij import IJ
+
+CHANNEL = 2
+LAMBDA_FLAT = 0.50
+LAMBDA_DARK = 0.50
+image = IJ.getImage()
+width, height, nChannels, nSlices, nFrames = image.getDimensions()
+spotsChannelImage = Duplicator().run(image, CHANNEL, CHANNEL, 1, nSlices, 1, nFrames)
+title = spotsChannelImage.getTitle()
+IJ.run(spotsChannelImage, "BaSiC ", "processing_stack=[" + spotsChannelImage.getTitle() + "] flat-field=None dark-field=None shading_estimation=[Estimate shading profiles] shading_model=[Estimate both flat-field and dark-field] setting_regularisationparametes=Automatic temporal_drift=[Replace with zero] correction_options=[Compute shading and correct images] lambda_flat=" + LAMBDA_FLAT + " lambda_dark=" + LAMBDA_DARK)
+IJ.selectImage()

volker/toolsets/measure_intensity_without_spots/export_wells.py

@@ -2,48 +2,19 @@
 from ij import ImagePlus
 from ij import ImageStack 
 from ij.io import FileSaver
+from ij.io import OpenDialog
 from ij.plugin import RGBStackMerge
 from loci.plugins import BF
-from loci.formats import ImageReader
-from loci.plugins.in import ImportProcess
 from loci.plugins.in import ImporterOptions
+from loci.formats import ImageReader
+from fr.cnrs.mri.cialib.conversion import BFWellsSeriesToTifStackSeries
 
-def main():
-    PATH = "/home/baecker/Documents/mri/in/marina/Quantification fluorescence/iHCS2301104-07-1et2-col2b-10X_Plate_45944/iHCS2301104-07-1et2-col2b-10X.HTD"
-    OUT_PATH = os.path.dirname(PATH)
-    OUT_PATH = os.path.join(OUT_PATH, "export")
-
-    if not os.path.exists(OUT_PATH):
-        os.makedirs(OUT_PATH)
-
-    CHANNELS = 2    
-    options = ImporterOptions()
-    options.setId(PATH)
-    options.setOpenAllSeries(True)
-    options.setSplitChannels(True)
-    images = list(BF.openImagePlus(options))
-    c0Stack = ImageStack(images[0].getWidth(), images[0].getHeight())
-    c1Stack = ImageStack(images[0].getWidth(), images[0].getHeight())
-    lastWell = None
-    title = ""
-    c0Images = [image for i, image in enumerate(images) if i%2==0]
-    c1Images = [image for i, image in enumerate(images) if i%2==1]
-    for c0Image, c1Image in zip(c0Images, c1Images):
-        print(c0Image.getTitle(), c1Image.getTitle())
-        title = c0Image.getTitle()
-        well = title.split("Well ")[1].split(" Field")[0]
-        if well == lastWell or lastWell==None: 
-            c0Stack.addSlice(c0Image.getProcessor())
-            c1Stack.addSlice(c1Image.getProcessor())
-        else:
-            imageC0 = ImagePlus(title, c0Stack)
-            imageC1 = ImagePlus(title.replace("C=0", "C=1"), c1Stack)
-            resultImage = RGBStackMerge.mergeChannels([imageC0, imageC1], False)
-            saver = FileSaver(resultImage)
-            saver.saveAsTiffStack(os.path.join(OUT_PATH, title.replace(" - C=0", "")))
-            c0Stack = ImageStack(images[0].getWidth(), images[0].getHeight())
-            c1Stack = ImageStack(images[0].getWidth(), images[0].getHeight())
-        lastWell = well
-
+def main():    
+    od = OpenDialog("Choose a file", None)
+    folder = od.getDirectory()
+    file = od.getFileName()
+    path = folder + file
+    converter = BFWellsSeriesToTifStackSeries(path)
+    converter.run()
 
 main()

volker/toolsets/measure_intensity_without_spots/measure_intensity_without_spots.ijm

@@ -13,46 +13,62 @@ macro "Measure Intensity Without Spots Help Action Tool - C000D0eDf8DfdDfeDffC02
 }
 
 
-macro "Remove Background (f1) Action Tool - C000T4b12r" {
+macro "Convert bioformats wells to tif series (f1) Action Tool - C000T4b12c" {
+    convertWells()
+}
+
+
+macro "Convert bioformats wells to tif series [F1]" {
+    convertWells()
+}
+
+
+macro "Remove Background (f2) Action Tool - C000T4b12r" {
     removeBackground();
 }
 
 
-macro "Remove Background [f1]" {
+macro "Remove Background [f2]" {
     removeBackground();
 }
 
 
-macro "Measure Image (f2) Action Tool - C000T4b12m" {
+macro "Measure Image (f3) Action Tool - C000T4b12m" {
     measureImage();
 }
 
 
-macro "measure image [F2]" {
+macro "measure image [F3]" {
     measureImage();
 }
 
 
-macro "Measure Image (f2) Action Tool Options" {
+macro "Measure Image (f3) Action Tool Options" {
     showMeasureIntensityOptions();
 }
 
 
-macro "Jump To Selected Label (f3) Action Tool - C000T4b12j" {
+macro "Jump To Selected Label (f4) Action Tool - C000T4b12j" {
     jumpToSelectedLabel();
 }
 
 
-macro "Jump To Selected Label (f3) Action Tool Options" {
+macro "Jump To Selected Label (f4) Action Tool Options" {
     showJumpToSeletedLabelOptions();
 }
 
 
-macro "jump to selected label [F2]" {
+macro "jump to selected label [F4]" {
     jumpToSelectedLabel();
 }
 
 
+
+function convertWells() {
+    run("export wells");
+}
+
+
 function showMeasureIntensityOptions() {
     call("ij.Prefs.set", "mri.options.only", "true");
     run("measure without spots");