first complete version

volker/toolsets/measure_intensity_without_spots/jump_to_label.py

@@ -79,7 +79,7 @@ def loadOptions():
         if "=" in option:
             value = parts[1]
         if key=="label":
-            Label = int(value)
+            LABEL = int(value)
         if key=="zoom":
             NR_OF_ZOOM_OUTS = int(value)
 

volker/toolsets/measure_intensity_without_spots/measure_intensity_without_spots.ijm

@@ -70,6 +70,11 @@ macro "Remove Background [f2]" {
 }
 
 
+macro "Remove Background (f2) Action Tool Options" {
+    showRemoveBackgroundOptions();
+}
+
+
 macro "Measure Image (f3) Action Tool - C000T4b12m" {
     measureImage();
 }
@@ -170,6 +175,13 @@ function convertWells() {
 }
 
 
+function showRemoveBackgroundOptions() {
+    call("ij.Prefs.set", "mri.options.only", "true");
+    run("remove background");
+    call("ij.Prefs.set", "mri.options.only", "false");  
+}
+
+
 function showMeasureIntensityOptions() {
     call("ij.Prefs.set", "mri.options.only", "true");
     run("measure without spots");
@@ -212,14 +224,22 @@ function loadOptions(path) {
 function jumpToSelectedLabel() {
     call("ij.Prefs.set", "mri.options.only", "false");   
     row = Table.getSelectionStart;
-    col = Table.getColumn("Label"); 
-    label =col[row];
+    label = LABEL
+    if (row > -1) {
+        col = Table.getColumn("Label"); 
+        label =col[row];
+    }
     zoom = NR_OF_ZOOM_OUT;
     pluginsPath = getDirectory("plugins");
     path = pluginsPath + "Measure-Intensity-Without-Spots/jtl-options.txt";
     if (File.exists(path)) {
-        optionsString = File.openAsString(path);    
+        optionsString = File.openAsString(path);   
         parts = split(optionsString, " ");
+        if (row == -1) {
+            parts0 = split(parts[0], "=");
+            labelTxt = parts0[1];
+            label = labelTxt.trim();
+        }
         parts = split(parts[1], "=");
         zoomTxt = parts[1];
         zoom = zoomTxt.trim();

volker/toolsets/measure_intensity_without_spots/measure_without_spots.py

@@ -12,6 +12,7 @@
 NUCLEUS_MIN_AREA = 50
 SHOW_LABELS = False
 SAVE_OPTIONS = True
+ADDITIONAL_OPTIONS = []
 URL = "https://github.com/MontpellierRessourcesImagerie/imagej_macros_and_scripts/wiki/Measure-Intensity-Without-Spots"
 
 
@@ -42,20 +43,26 @@ def main():
 
 
 def showDialog():
-    global NUCLEI_CHANNEL, SIGNAL_CHANNEL, NUCLEUS_MIN_AREA, METHODS, METHOD, SAVE_OPTIONS, URL
+    global NUCLEI_CHANNEL, SIGNAL_CHANNEL, NUCLEUS_MIN_AREA, METHODS, METHOD, ADDITIONAL_OPTIONS, SAVE_OPTIONS, URL
 
     cls = NucleiSegmentationMethod
     methodClasses = list(set(cls.__subclasses__()))
+    ADDITIONAL_OPTIONS = []
     for methodClass in methodClasses:
-        print(methodClass.name(), methodClass.options())
-
+        if methodClass.name() == METHOD:
+            for option in methodClass.options().values():
+                ADDITIONAL_OPTIONS.append(option)
+    print(ADDITIONAL_OPTIONS)    
     if  os.path.exists(getOptionsPath()):
         loadOptions()
     gd = GenericDialog("Measure Without Spots Options"); 
     gd.addNumericField("Nuclei Channel: ", NUCLEI_CHANNEL)
     gd.addNumericField("Signal Channel: ", SIGNAL_CHANNEL)
     gd.addNumericField("Min. Area Nucleus: ", NUCLEUS_MIN_AREA)
     gd.addChoice("Method: ", METHODS, METHOD)
+    for option in ADDITIONAL_OPTIONS:
+        if option['type'] == int or option['type'] == float:
+            gd.addNumericField(option['name'] + ': ' , option['value'])        
     gd.addCheckbox("Save Options", SAVE_OPTIONS)
     gd.addHelp(URL)
     gd.showDialog()
@@ -65,6 +72,9 @@ def showDialog():
     SIGNAL_CHANNEL = int(gd.getNextNumber())
     NUCLEUS_MIN_AREA = float(gd.getNextNumber())
     METHOD = gd.getNextChoice()
+    for option in ADDITIONAL_OPTIONS:
+        if option['type'] == int or option['type'] == float:
+            option['value'] = option['type'](gd.getNextNumber())
     SAVE_OPTIONS = gd.getNextBoolean()
     if SAVE_OPTIONS:
         saveOptions()
@@ -83,11 +93,13 @@ def getOptionsString():
     optionsString = optionsString + " signal=" + str(SIGNAL_CHANNEL)
     optionsString = optionsString + " min.=" + str(NUCLEUS_MIN_AREA)
     optionsString = optionsString + " method.=" + str(METHOD)
+    for option in ADDITIONAL_OPTIONS:
+        optionsString = optionsString + " " + option['name'] + "=" + str(option['value'])
     return optionsString    
 
 
 def loadOptions(): 
-    global NUCLEI_CHANNEL, SIGNAL_CHANNEL, NUCLEUS_MIN_AREA, METHOD
+    global NUCLEI_CHANNEL, SIGNAL_CHANNEL, NUCLEUS_MIN_AREA, METHOD, ADDITIONAL_OPTIONS
 
     optionsPath = getOptionsPath()
     optionsString = IJ.openAsString(optionsPath)
@@ -107,6 +119,9 @@ def loadOptions():
             NUCLEUS_MIN_AREA = float(value)
         if key=="method":
             METHOD = str(value)
+        for additionalOption in ADDITIONAL_OPTIONS:
+            if key==additionalOption['name']:
+                additionalOption['value'] = additionalOption['type'](value)
 
 
 def saveOptions():

volker/toolsets/measure_intensity_without_spots/quantification.py

@@ -258,12 +258,12 @@ class SubtractGaussianAndThresholdSegmentation(NucleiSegmentationMethod):
 
     @classmethod
     def name(cls):
-        return "subtract Gaussian and threshold"
+        return "subtract_Gaussian_and_threshold"
 
 
     @classmethod
     def options(cls):
-        return { 1 : {'name': 'sigma', 'defaultValue': 40.86, 'type' : int}}
+        return { 1 : {'name': 'sigma', 'value': 40.86, 'type' : float}}
 
 
     def __init__(self, image):

volker/toolsets/measure_intensity_without_spots/remove_background.py

@@ -1,21 +1,30 @@
+import os
 from ij import IJ
+from ij import Prefs
+from ij.gui import GenericDialog
 from ij import WindowManager
 from ij.plugin import Duplicator
 from ij.plugin import RGBStackMerge
 
 
-SPOTS_CHANNEL = 2
+SIGNAL_CHANNEL = 2
 NUCLEI_CHANNEL = 1
 LAMBDA_FLAT = 0.50
 LAMBDA_DARK = 0.50
 SAVE_OPTIONS = True
 URL = "https://github.com/MontpellierRessourcesImagerie/imagej_macros_and_scripts/wiki/Measure-Intensity-Without-Spots"
 
-def main():
 
+def main():
+    optionsOnly = Prefs.get("mri.options.only", "false")
+    if not showDialog():
+        return
+    if optionsOnly=="true":
+        return
+    return
     image = IJ.getImage()
     width, height, nChannels, nSlices, nFrames = image.getDimensions()
-    spotsChannelImage = Duplicator().run(image, SPOTS_CHANNEL, SPOTS_CHANNEL, 1, nSlices, 1, nFrames)
+    spotsChannelImage = Duplicator().run(image, SIGNAL_CHANNEL, SIGNAL_CHANNEL, 1, nSlices, 1, nFrames)
     spotsChannelImage.show()
     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=" + str(LAMBDA_FLAT) + " lambda_dark=" + str(LAMBDA_DARK))
@@ -32,10 +41,79 @@ def main():
     resultImage.setTitle(title)
     resultImage.show()
 
+
+def showDialog():
+    global NUCLEI_CHANNEL, SIGNAL_CHANNEL, LAMBDA_FLAT, SAVE_OPTIONS, LAMBDA_DARK, URL
+
+    if  os.path.exists(getOptionsPath()):
+        loadOptions()
+    gd = GenericDialog("Remove Background Options"); 
+    gd.addNumericField("Nuclei Channel: ", NUCLEI_CHANNEL)
+    gd.addNumericField("Signal Channel: ", SIGNAL_CHANNEL)
+    gd.addNumericField("Lambda_Flat: ", LAMBDA_FLAT)
+    gd.addNumericField("Lambda_Dark: ", LAMBDA_DARK)
+    gd.addCheckbox("Save Options", SAVE_OPTIONS)
+    gd.addHelp(URL)
+    gd.showDialog()
+    if gd.wasCanceled():
+        return False
+    NUCLEI_CHANNEL = int(gd.getNextNumber())
+    SIGNAL_CHANNEL = int(gd.getNextNumber())
+    LAMBDA_FLAT = float(gd.getNextNumber())
+    LAMBDA_DARK = float(gd.getNextNumber())
+    SAVE_OPTIONS = gd.getNextBoolean()
+    if SAVE_OPTIONS:
+        saveOptions()
+    return True
+
+
+def getOptionsPath():
+    pluginsPath = IJ.getDirectory("plugins");
+    optionsPath = pluginsPath + "Measure-Intensity-Without-Spots/rb-options.txt";
+    return optionsPath;
+
 
+def getOptionsString():
+    optionsString = ""
+    optionsString = optionsString + "nuclei=" + str(NUCLEI_CHANNEL)
+    optionsString = optionsString + " signal=" + str(SIGNAL_CHANNEL)
+    optionsString = optionsString + " lambda_flat=" + str(LAMBDA_FLAT)
+    optionsString = optionsString + " lambda_dark=" + str(LAMBDA_DARK)
+    return optionsString 
+
+
 def closeWindow(title):
     win = WindowManager.getWindow(title)
     win.close()
+
+
+def loadOptions(): 
+    global NUCLEI_CHANNEL, SIGNAL_CHANNEL, LAMBDA_FLAT, LAMBDA_DARK
+
+    optionsPath = getOptionsPath()
+    optionsString = IJ.openAsString(optionsPath)
+    optionsString = optionsString.replace("\n", "")
+    options = optionsString.split(" ")
+    for option in options:
+        parts = option.split("=")
+        key = parts[0]
+        value = ""
+        if "=" in option:
+            value = parts[1]
+        if key=="nuclei":
+            NUCLEI_CHANNEL = int(value)
+        if key=="signal":
+            SIGNAL_CHANNEL = int(value)
+        if key=="lambda_flat":
+            LAMBDA_FLAT = float(value)
+        if key=="lambda_dark":
+            LAMBDA_DARK = float(value)
+
+
+def saveOptions():
+    optionsString = getOptionsString()
+    optionsPath = getOptionsPath()
+    IJ.saveString(optionsString, getOptionsPath())
 
 
 main()