diff --git a/src/ij-plugins/Ipr/Lipase/Compute_Globules_Area.py b/src/ij-plugins/Ipr/Lipase/Compute_Globules_Area.py index bc6ef1e..e7a93bc 100644 --- a/src/ij-plugins/Ipr/Lipase/Compute_Globules_Area.py +++ b/src/ij-plugins/Ipr/Lipase/Compute_Globules_Area.py @@ -4,6 +4,7 @@ #@output ImagePlus OUTPUT_PLOT """This script is supposed to be launched from fiji's jython interpreter +This plugin estimates the global area of globules """ @@ -15,16 +16,41 @@ print('python version %s' % sys.version) # prints python version from lipase.settings import UserSettings # from lipase import Lipase, ImageLogger -from lipase.imageengine import IImageEngine, PixelType, StackImageFeeder +from lipase.imageengine import IImageEngine, PixelType, StackImageFeeder, IImageProcessingDebugger from lipase.imagej.ijimageengine import IJImageEngine from lipase.lipase import UserProvidedBackground, GlobulesAreaEstimator - +# from lipase.improc.improlis import IMovieProcessListener # from ij import IJ # pylint: disable=import-error # from ij.gui import GenericDialog, DialogListener # pylint: disable=import-error # from java.awt.event import ItemListener # pylint: disable=import-error import ij.gui from jarray import zeros, array + +class IsParticleCollector(IImageProcessingDebugger): + + def __init__(self, num_frames): + IImageProcessingDebugger.__init__(self) + ie = IImageEngine.get_instance() + self.is_particle = None + self.num_frames = num_frames + self.frame_index = 0 + + def on_image(self, image, image_id): + # print('IsParticleCollector.on_image : image_id = %s' % image_id) + if image_id == 'is_particle': + ie = IImageEngine.get_instance() + if self.is_particle is None: + self.is_particle = ie.create_hyperstack(width=image.get_width(), height=image.get_height(), num_channels=1, num_slices=1, num_frames=self.num_frames, pixel_type=PixelType.U8) + self.is_particle.set_image(image=image, frame_index=self.frame_index) + print("IsParticleCollector.on_image : %f %f" % image.get_value_range()) + self.is_particle.set_image(image=image, frame_index=self.frame_index) + self.frame_index += 1 + + def on_hyperstack(self, hyperstack, hyperstack_id): + # print('IsParticleCollector.on_hyperstack : hyperstack_id = %s' % hyperstack_id) + pass + def run_script(): global INPUT_STACK # pylint:disable=global-variable-not-assigned global INPUT_BACKGROUND # pylint:disable=global-variable-not-assigned @@ -41,8 +67,8 @@ def run_script(): background_estimator = UserProvidedBackground(background_image=src_background) processor = GlobulesAreaEstimator(background_estimator=background_estimator, particle_threshold=PARTICLE_THRESHOLD) # pylint: disable=undefined-variable - - results = processor.detect_particles(src_hyperstack) + is_particle_collector = IsParticleCollector(num_frames = src_hyperstack.num_frames()) + results = processor.detect_particles(src_hyperstack, image_proc_debugger=is_particle_collector) # save_hdf5_file('results.h5', results) # results file could be checked with "h5dump --xml ./lipase.git/results.h5" @@ -50,8 +76,16 @@ def run_script(): x = array(results['frame index'].elements, 'f') y = array(results['globules_area_ratio'].elements, 'f') - plot = ij.gui.Plot('my_title', 'frame', 'globules area ratio', x, y) + plot = ij.gui.Plot('globules area graph', 'frame', 'globules area ratio', x, y) plot.show() + + print("Compute_Globules_Area is_particle_collector.is_particle size : %d" % (is_particle_collector.is_particle.num_frames())) + first_frame = is_particle_collector.is_particle.get_image(frame_index=0, slice_index=0, channel_index=0) + print("Compute_Globules_Area is_particle_collector.is_particle size : %f %f" % first_frame.get_value_range()) + + is_particle_collector.is_particle.hyperstack.setTitle('is_particle') + is_particle_collector.is_particle.hyperstack.show() + OUTPUT_PLOT = plot diff --git a/src/lipase/improc/__init__.py b/src/lipase/improc/__init__.py deleted file mode 100644 index 3130f1a..0000000 --- a/src/lipase/improc/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from .improlis import MovieProcessDebugger diff --git a/src/lipase/improc/graphing.py b/src/lipase/improc/graphing.py deleted file mode 100644 index 382351a..0000000 --- a/src/lipase/improc/graphing.py +++ /dev/null @@ -1,106 +0,0 @@ -# -*- coding: utf-8 -*- -""" - installation des modules nécéssaires sur macos x : - sudo port install opencv +python27 - sudo port install py-pyqt4 - sudo port install py-matplotlib - -""" -from matplotlib import pyplot -from matplotlib.backends.backend_pdf import PdfPages - -def setLatexLookingFonts(): - import matplotlib - matplotlib.rcParams['mathtext.fontset'] = 'stix' - matplotlib.rcParams['font.family'] = 'STIXGeneral' - #matplotlib.pyplot.title(r'ABC123 vs $\mathrm{ABC123}^{123}$') - -class Signal: - def __init__(self, signal, name=None): - self.m_signalValues = signal - self.m_name = name - -class Point2D(object): - def __init__(self, x, y): - self.m_x = x - self.m_y = y - @property - def x(self): - return self.m_x - @property - def y(self): - return self.m_y - -class ScatterPlot(object): - def __init__(self, xAxisDesc = None, yAxisDesc = None): - self.m_points = [] - self.m_xAxisDesc = xAxisDesc - self.m_yAxisDesc = yAxisDesc - def append(self, point2d ): - self.m_points.append(point2d) - @property - def xAxisDesc(self): - return self.m_xAxisDesc - @property - def yAxisDesc(self): - return self.m_yAxisDesc - - def setXAxisDesc(self, description): - self.m_xAxisDesc = description - def setYAxisDesc(self, description): - self.m_yAxisDesc = description - def __iter__(self): - return iter(self.m_points) - -def saveScatterPlot( scatterPlot, pdfFileName): - setLatexLookingFonts() - fig = pyplot.figure() - pyplot.subplot(1,1,1) - x = [] - y = [] - for point in scatterPlot: - x.append( point.x ) - y.append( point.y ) - pyplot.scatter(x, y, marker='x') - if scatterPlot.xAxisDesc is not None: - pyplot.xlabel(scatterPlot.xAxisDesc) - if scatterPlot.yAxisDesc is not None: - pyplot.ylabel(scatterPlot.yAxisDesc) - - #print('saving to '+pdfFileName) - pp = PdfPages(pdfFileName) - pp.savefig( fig ) - pp.close() - pyplot.close(fig) - - -def saveGraph(signal, pdfFileName): - setLatexLookingFonts() - fig = pyplot.figure() - pyplot.subplot(1,1,1) - pyplot.plot(signal, marker='x') - - print('saving to '+pdfFileName) - pp = PdfPages(pdfFileName) - pp.savefig( fig ) - pp.close() - pyplot.close(fig) - -def saveMultiGraph(signals, pdfFileName): - setLatexLookingFonts() - fig = pyplot.figure() - pyplot.subplot(1,1,1) - for signal in signals: - print('plotting signal %s' % str(signal.m_signalValues.shape)) - pyplot.plot(signal.m_signalValues, label=signal.m_name) - print('saving to '+pdfFileName) - pyplot.legend() - pp = PdfPages(pdfFileName) - pp.savefig( fig ) - pp.close() - pyplot.close(fig) - - - - - diff --git a/src/lipase/improc/improlis.py b/src/lipase/improc/improlis.py deleted file mode 100644 index eb0458c..0000000 --- a/src/lipase/improc/improlis.py +++ /dev/null @@ -1,238 +0,0 @@ -# -*- coding: utf-8 -*- -""" - installation des modules nécéssaires sur macos x : - sudo port install opencv +python27 - sudo port install py-pyqt4 - sudo port install py-matplotlib - -""" -#from PyQt4.QtGui import * -#from PyQt4.QtCore import * -#import sys - -import cv2 -#from cv2 import cv -import numpy -import os -import sys -#from matplotlib import pyplot as plt -#from matplotlib.backends.backend_pdf import PdfPages - -sys.path.append('../Libraries/python') -import scene2d -import graphing - -class Line2D(object): - def __init__( self, point1, point2 ): - self.m_point1 = point1 - self.m_point2 = point2 - -class IImageProcessListener(object): - """ - an abstract base class that handle events that happen during an image processing. This provides a flexible way to debug image processing - """ - def __init__(self): - self.m_imageIndex = 0 - def onSignal(self, signal, signalName): - """ - a new signal (1d array) has just been computed - """ - assert( False ) - def onImage(self, image, imageName): - """ - a new image has just been computed - """ - assert( False ) - -class NullImageProcessListener(IImageProcessListener): - def __init__(self): - IImageProcessListener.__init__( self ) - def onSignal(self, signal, signalName): - pass - def onBaseImage(self, image, imageName=''): - pass - def onImage(self, image, imageName): - pass - def onPoint(self, point, layerPath, label=None ): - pass - def onLine(self, line, layerPath, label=None ): - pass - def onCircle(self, circle, layerPath, label=None ): - pass - -class ImageProcessDebugger(IImageProcessListener): - def __init__(self, outputFolder='./debug'): - IImageProcessListener.__init__( self ) - self.m_scene = None - self.m_baseImageName = None - self.setOutputFolder(outputFolder) - - def __del__(self): - #assert( self.m_scene is not None ) - if self.m_scene: - self.m_scene.saveAsSvg('%s/%s.svg' % (self.m_outputFolder, self.m_baseImageName)) - self.m_scene = None - def setOutputFolder(self, outputFolderPath): - if self.m_scene: - self.m_scene.saveAsSvg('%s/%s.svg' % (self.m_outputFolder, self.m_baseImageName)) - self.m_scene = None - self.m_outputFolder = outputFolderPath - pathParts = self.m_outputFolder.split('/') - path = '' - for i in range(len(pathParts)): - if i != 0: - path += '/' - path += pathParts[i] - try: - os.mkdir(path) - except (OSError): # this exception is raised if the folder already exists - pass - def onSignal(self, signal, signalName): - graphing.saveGraph(signal, '%s/%s.pdf' % (self.m_outputFolder, signalName)) - def onSignals(self, signals, signalName): - graphing.saveMultiGraph(signals, '%s/%s.pdf' % (self.m_outputFolder, signalName)) - def onImage(self, image, imageName): - #plt.subplot(1,1,1),plt.imshow(contourImage,cmap = 'gray') - #plt.title('Sobel X'), plt.xticks([]), plt.yticks([]) - #plt.show() - filePath = '%s/%s.tif' % (self.m_outputFolder, imageName) - saveImage( image, filePath ) - def onBaseImage(self, image, imageName=''): - assert(imageName != '') - self.m_baseImageName=imageName - filePath = '%s/%s.png' % (self.m_outputFolder, imageName) - saveImage( image, filePath ) - self.m_scene = scene2d.Scene() - assert( self.m_scene is not None ) - if self.m_scene: - self.m_scene.setBaseImage(scene2d.Image(filePath)) - def onPoint(self, point, layerPath, label=None ): - assert( self.m_scene ) - self.m_scene.getLayer(layerPath).addChild(scene2d.Point(point, label)) - def onLine(self, line, layerPath, label=None ): - assert( self.m_scene ) - self.m_scene.getLayer(layerPath).addChild(scene2d.Line(line, label)) - def onCircle(self, circle, layerPath, label=None ): - assert( self.m_scene ) - self.m_scene.getLayer(layerPath).addChild(scene2d.Circle(circle, label)) - - -class IMovieProcessListener(object): - """ - an abstract base class that handle events that happen durin a movie image processing. This provides a flexible way to debug imageprocessing - """ - def __init__(self, imageProcessListener ): - self.m_imageIndex = 0 - self.m_imageProcessListener = imageProcessListener - def onImageProcessingStart(self): - """ - the processing of a new image starts - """ - self.m_imageIndex += 1 - def onImageProcessingEnd(self): - """ - the processing of a new image ends - """ - pass - def onSignal(self, signal, signalName): - """ - a new signal (1d array) has just been computed - """ - self.m_imageProcessListener.onSignal( signal, signalName ) - def onImage(self, image, imageName): - """ - a new image has just been computed - """ - self.m_imageProcessListener.onImage( image, imageName ) - -class NullMovieProcessListener(IMovieProcessListener): - def __init__(self): - IMovieProcessListener.__init__( self, NullImageProcessListener() ) - def onSignal(self, signal, signalName): - pass - def onImage(self, image, imageName): - pass - -def saveImage(image, filePath): - print('%s original image type : %s range=(%f:%f)' % (filePath, str(image.dtype), image.min(), image.max())) - if image.dtype == numpy.bool: - cv2.imwrite(filePath, image.astype(numpy.uint8)*255) - elif image.dtype == numpy.uint16: - fileExt = filePath.split('.')[-1] - if fileExt == 'tif': - # tif file format supports 16 bits per pixel - cv2.imwrite(filePath, image) - else: - u8Image = cv2.normalize(image, alpha=0.0, beta=255.0, norm_type=cv2.NORM_MINMAX, dtype=cv2.CV_8U) - cv2.imwrite(filePath, u8Image) - elif image.dtype == numpy.float32 or image.dtype == numpy.float64: - print('image range : %d-%d' % (image.min(), image.max())) - u8Image = cv2.normalize(image, numpy.array(image.shape, dtype=numpy.uint8), alpha=0.0, beta=255.0, norm_type=cv2.NORM_MINMAX, dtype=cv2.CV_8U) - print('u8Image range : %d-%d' % (u8Image.min(), u8Image.max())) - cv2.imwrite(filePath, u8Image) - elif image.dtype == numpy.int32: - print('image range : %d-%d' % (image.min(), image.max())) - u8Image = cv2.normalize(image, numpy.array(image.shape, dtype=numpy.uint8), alpha=0.0, beta=255.0, norm_type=cv2.NORM_MINMAX, dtype=cv2.CV_8U) - print('u8Image range : %d-%d' % (u8Image.min(), u8Image.max())) - cv2.imwrite(filePath, u8Image) - else: - #assert( False ) - cv2.imwrite(filePath, image) - - - -class MovieProcessDebugger(IMovieProcessListener): - def __init__(self): - IMovieProcessListener.__init__( self, ImageProcessDebugger() ) - self.m_outputFolder='./debug' - self.m_scene = None - try: - os.mkdir(self.m_outputFolder) - except (OSError): # this exception is raised if the folder already exists - pass - def onImageProcessingStart(self): - """ - the processing of a new image starts - """ - IMovieProcessListener.onImageProcessingStart(self) - self.m_imageProcessListener.setOutputFolder( '%s/image%d' % (self.m_outputFolder, self.m_imageIndex) ) - - def onImageProcessingEnd(self): - IMovieProcessListener.onImageProcessingEnd(self) - self.m_imageProcessListener.setOutputFolder( None ) - def onSignal(self, signal, signalName): - self.m_imageProcessListener.onSignal( signal, signalName ) - def onSignals(self, signals, signalName): - self.m_imageProcessListener.onSignal( signals, signalName ) - def onImage(self, image, imageName): - self.m_imageProcessListener.onImage( image, imageName ) - def onBaseImage(self, image, imageName): - self.m_imageProcessListener.onBaseImage( image, imageName ) - def onPoint(self, point, layerPath, label=None ): - self.m_imageProcessListener.onPoint( image, point, layerPath, label ) - def onCircle(self, circle, layerPath, label=None ): - self.m_imageProcessListener.onPoint( image, circle, layerPath, label ) - - -class IImageProcessor(object): - - def __init__(self, movieProcessListener = NullMovieProcessListener()): - self.m_movieProcessListener = movieProcessListener - - def processImage(self, image): - assert( False ) # this method is not supposed to be called - - def get_image_process_listener(self): - return self.m_movieProcessListener - - -def findEdges(image): - sx = cv2.Sobel(image, cv2.CV_32F, dx=1, dy=0, ksize=3) - sy = cv2.Sobel(image, cv2.CV_32F, dx=0, dy=1, ksize=3) - return numpy.sqrt(sx*sx + sy*sy) - - - - - - diff --git a/src/lipase/improc/scene2d.py b/src/lipase/improc/scene2d.py deleted file mode 100644 index 3e5269c..0000000 --- a/src/lipase/improc/scene2d.py +++ /dev/null @@ -1,166 +0,0 @@ -# -*- coding: utf-8 -*- -import cv2 - -class ISceneNodeVisitor(object): - def __init__(self): - pass - - def visitPoint(self, point): - assert( False ) - - def visitImage(self, image): - assert( False ) - - def visitLayer(self, layer): - assert( False ) - - def visitScene(self, scene): - assert( False ) - - def visitLine(self, line): - assert( False ) - - - -class ISceneNode(object): - def __init__(self): - pass - - def onVisit(self, visitor ): - assert( False ) - -class Point(ISceneNode): - def __init__(self, coords, label = None): - self.m_coords = coords - self.m_label = label - - def onVisit( self, visitor ): - visitor.visitPoint( self ) - -class Line(ISceneNode): - def __init__(self, line, label = None): - self.m_from = line[0] - self.m_to = line[1] - self.m_label = label - - def onVisit( self, visitor ): - visitor.visitLine( self ) - -class Circle(ISceneNode): - def __init__(self, circle, label = None): - self.m_center = (circle[0], circle[1]) - self.m_radius = circle[2] - self.m_label = label - - def onVisit( self, visitor ): - visitor.visitCircle( self ) - -class Image(ISceneNode): - def __init__(self, imageFilePath): - self.m_imageFilePath = imageFilePath - - def onVisit(self, visitor ): - visitor.visitImage( self ) - - def getFilePath(self): - return self.m_imageFilePath - - def getSize(self): - cv_img = cv2.imread(self.m_imageFilePath, cv2.IMREAD_ANYDEPTH) - return cv_img.shape - -class Layer(ISceneNode): - def __init__(self, layerName): - self.m_name = layerName - self.m_children = [] - self.m_layers = {} - - def getName(self): - return self.m_name - - def addChild(self, childNode): - self.m_children.append( childNode ) - - def onVisit(self, visitor ): - visitor.visitLayer( self ) - - def addLayer(self, layer): - print('adding layer %s' % layer.getName()) - self.m_layers[ layer.getName() ] = layer - - - -class Scene(ISceneNode): - def __init__(self): - self.m_image = None - self.m_rootLayer = Layer('root') - - def onVisit(self, visitor ): - visitor.visitScene( self ) - - def setBaseImage( self, image ): - self.m_image = image - - def getLayer(self, layerPath): - pathParts = layerPath.split('/') - parentLayer = self.m_rootLayer - for layerName in pathParts: - if layerName not in parentLayer.m_layers: - parentLayer.addLayer( Layer(layerName) ) - parentLayer = parentLayer.m_layers[layerName] - return parentLayer - - def saveAsSvg(self, filePath): - visitor = SvgExporter( filePath ) - self.onVisit(visitor) - -class SvgExporter(ISceneNodeVisitor): - def __init__(self, svgFilePath): - self.m_svgFilePath = svgFilePath - - def visitPoint(self, point): - radius = 1.0 - self.m_f.write('\n' % (point.m_coords[0], point.m_coords[1], radius) ) - if point.m_label is not None : - self.m_f.write('%s\n' % (point.m_coords[0], point.m_coords[1], point.m_label) ) - - def visitLine(self, line): - radius = 1.0 - self.m_f.write('\n' % (line.m_from[0], line.m_to[0], line.m_from[1], line.m_to[1]) ) - if line.m_label is not None : - self.m_f.write('%s\n' % (line.m_from[0], line.m_from[1], point.m_label) ) - - def visitCircle(self, circle): - radius = 1.0 - self.m_f.write('\n' % (circle.m_center[0], circle.m_center[1], circle.m_radius) ) - if circle.m_label is not None : - self.m_f.write('%s\n' % (circle.m_center[0], circle.m_center[1], point.m_label) ) - - def visitImage(self, image): - imageSize = image.getSize() - self.m_f.write('\n' % (image.getFilePath().split('/')[-1], imageSize[1], imageSize[0]) ) - - def visitLayer(self, layer): - self.m_f.write('\n' % layer.getName()) - for child in layer.m_children: - child.onVisit( self ) - for layer in layer.m_layers.itervalues(): - layer.onVisit( self ) - self.m_f.write('\n') - - def visitScene(self, scene): - with open(self.m_svgFilePath, 'wt') as self.m_f: - print('exporting scene2d as %s' % self.m_svgFilePath) - self.m_f.write('') - self.m_f.write('') - self.m_f.write('') - self.m_f.write('') - self.m_f.write('') - if scene.m_image is not None: - scene.m_image.onVisit(self) - - scene.m_rootLayer.onVisit(self) - #f.write('') - self.m_f.write('') - - diff --git a/src/lipase/lipase.py b/src/lipase/lipase.py index 2296129..b30c262 100644 --- a/src/lipase/lipase.py +++ b/src/lipase/lipase.py @@ -173,7 +173,6 @@ class EmptyFrameBackgroundEstimator(IBackgroundEstimator): background_estimate = visible_traps_sequence.get_image(frame_index=self.empty_frame_index).clone() return background_estimate - class GlobulesAreaEstimator(object): """ An image processing suite targetted to visible images of traps with moving particles (globules) """ @@ -186,7 +185,7 @@ class GlobulesAreaEstimator(object): self.background_estimator = background_estimator self.particle_threshold = particle_threshold - def detect_particles(self, visible_traps_sequence): + def detect_particles(self, visible_traps_sequence, image_proc_debugger=NullDebugger()): """ :param IHyperStack visible_traps_sequence: :rtype: hdf5_data.Group @@ -206,6 +205,7 @@ class GlobulesAreaEstimator(object): particle_image = ie.subtract(visible_traps_sequence.get_image(frame_index=frame_index), background_image) abs_particle_image = ie.abs( particle_image ) is_particle = ie.threshold(abs_particle_image, self.particle_threshold) + image_proc_debugger.on_image(is_particle, 'is_particle') measured_mean_value = is_particle.get_mean_value() particle_pixel_value = 255.0 num_pixels = is_particle.get_width() * is_particle.get_height()