made lots of tests to attempt to use opencv's calcHist function
Due to the lack of documentation, I had to do a lot of tests to find out how to use opencv in jython, as the interface is not the same as in python... In the end, I managed to work out a set of arguments that deosn't cause an exception.
This commit is contained in:
parent
de1e837d60
commit
361fb552e7
279
lipase.py
279
lipase.py
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@ -5,7 +5,15 @@
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# It is the duty of the scripting framework to harvest
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# the 'name' parameter from the user, and then display
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# the 'greeting' output parameter, based on its type.
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from ij import IJ
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from ij import IJ # pylint: disable=import-error
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from ijopencv.ij import ImagePlusMatConverter # pylint: disable=import-error
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from ijopencv.opencv import MatImagePlusConverter # pylint: disable=import-error
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from ij import ImagePlus # pylint: disable=import-error
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import org.bytedeco.javacpp.opencv_core as opencv_core # pylint: disable=import-error
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import org.bytedeco.javacpp.opencv_imgproc as opencv_imgproc # pylint: disable=import-error
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from org.bytedeco.javacpp.opencv_imgcodecs import imread # pylint: disable=import-error
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# greeting = "Hello, " + name + "!"
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@ -36,6 +44,7 @@ from ij import IJ
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# - cond[5678] : condition non réalistes
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import json
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class Sequence(object):
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def __init__(self, catalog, sequence_id, micro_manager_metadata_file_path):
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self.catalog = catalog
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@ -45,6 +54,7 @@ class Sequence(object):
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with open(micro_manager_metadata_file_path, "r") as mmm_file:
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self.mmm = json.load(mmm_file, encoding='latin-1') # note : the micromanager metadata files are encoded in latin-1, not utf8 (see accents in comments)
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@property
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def num_frames(self):
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summary = self.mmm['Summary']
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@ -79,17 +89,48 @@ class Sequence(object):
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return '/'.join(self.micro_manager_metadata_file_path.split('/')[:-1])
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def get_image_file_path(self, channel_index, frame_index, z_index=0):
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'''
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:param int channel_index:
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:param int frame_index:
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:param int z_index:
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'''
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assert frame_index < self.num_frames
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assert channel_index < self.num_channels
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summary = self.mmm['Summary']
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frame_info = self.mmm['FrameKey-%d-%d-%d' % (frame_index, channel_index, z_index)]
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rel_file_path = frame_info['FileName']
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return self.get_root_path() + '/' + rel_file_path
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def get_channel_index(self, channel_id):
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'''
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:param str channel_id:
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'''
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summary = self.mmm['Summary']
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channel_index = summary['ChNames'].index(channel_id)
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return
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return channel_index
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def get_black(self):
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''' returns the black sequence related to the the sequence self
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:return Sequence:
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'''
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seqid_to_black = {
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'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0': 'res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0',
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'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2': 'res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0',
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}
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white_sequence = seqid_to_black[self.sequence_id]
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return self.catalog.sequences[white_sequence]
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def get_white(self):
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''' returns the white sequence related to the the sequence self
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:return Sequence:
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'''
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seqid_to_white = {
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'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0': 'res_soleil2018/white/white_24112018_2/Pos0',
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'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2': 'res_soleil2018/white/white_24112018_2/Pos0',
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}
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white_sequence = seqid_to_white[self.sequence_id]
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return self.catalog.sequences[white_sequence]
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def open_in_imagej(self):
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# ip = IJ.createHyperStack(title=self.sequence_id, width=self.width, height= self.height, channels=1, slices=1, frames=self.get_num_frames(), bitdepth=16)
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@ -107,6 +148,8 @@ class Sequence(object):
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for channel_index in range(self.num_channels):
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hyperstack.setPositionWithoutUpdate(channel_index + 1, 1, 1)
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IJ.run("Enhance Contrast", "saturated=0.35")
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return hyperstack
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class ImageCatalog(object):
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def __init__(self, raw_images_root):
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@ -117,7 +160,10 @@ class ImageCatalog(object):
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sequence_ids = []
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sequence_ids.append('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0')
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sequence_ids.append('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2')
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sequence_ids.append('res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0')
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sequence_ids.append('res_soleil2018/DARK/DARK_40X_zstack_vis_327-353_1/Pos0')
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# sequence_ids.append('res_soleil2018/white/white_24112018_1/Pos0') # this sequence seems broken (only 5 images while there's supposed to be 201 frames)
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sequence_ids.append('res_soleil2018/white/white_24112018_2/Pos0')
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@ -134,25 +180,246 @@ class ImageCatalog(object):
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# def add_micromanager_metadata(self, micro_manager_metadata_file_path):
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# self.sequences[ micro_manager_metadata_file_path ] = Sequence(self, micro_manager_metadata_file_path)
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def test_opencv_calc_hist1():
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src_image = opencv_core.Mat([128, 128])
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histogram = opencv_imgproc.cvCalcHist(src_image) # pylint: disable=unused-variable
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# TypeError: cvCalcHist(): expected 2 or 4 args; got 1
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def test_opencv_calc_hist2():
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src_image = opencv_core.Mat([128, 128])
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histogram = opencv_core.Mat()
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opencv_imgproc.cvCalcHist(src_image, histogram)
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# TypeError: cvCalcHist(): 1st arg can't be coerced to org.bytedeco.javacpp.opencv_core$IplImage
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def test_opencv_calc_hist3():
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src_image = opencv_core.Mat([128, 128])
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histogram = opencv_imgproc.calcHist(src_image) # pylint: disable=unused-variable
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# TypeError: calcHist(): expected 6-8 or 10 args; got 1
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# ah: ./opencv/src/main/java/org/bytedeco/javacpp/opencv_imgproc.java seems to contain the list of 57 allowed calcHist sets of arguments, as the number of arguments match
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# [OK]graffy@pr079234:~/toto/javacpp-presets[19:45:41]>grep -A 5 calcHist ./opencv/src/main/java/org/bytedeco/javacpp/opencv_imgproc.java | sed -E 's/^[ ]*//g' | tr '\n' '`' | sed 's/,`/, /g' | tr '`' '\n' | grep '^@Namespace' | wc -l
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# 57
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# [OK]graffy@pr079234:~/toto/javacpp-presets[19:45:56]>grep -A 5 calcHist ./opencv/src/main/java/org/bytedeco/javacpp/opencv_imgproc.java | sed -E 's/^[ ]*//g' | tr '\n' '`' | sed 's/,`/, /g' | tr '`' '\n' | grep '^@Namespace' | head -2
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# @Namespace("cv") public static native void calcHist( @Const Mat images, int nimages, @Const IntPointer channels, @ByVal Mat mask, @ByVal Mat hist, int dims, @Const IntPointer histSize, @Cast("const float**") PointerPointer ranges, @Cast("bool") boolean uniform/*=true*/, @Cast("bool") boolean accumulate/*=false*/ );
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# @Namespace("cv") public static native void calcHist( @Const Mat images, int nimages, @Const IntPointer channels, @ByVal Mat mask, @ByVal Mat hist, int dims, @Const IntPointer histSize, @Const @ByPtrPtr FloatPointer ranges );
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# [OK]graffy@pr079234:~/toto/javacpp-presets[19:38:39]>grep -A 5 calcHist ./opencv/src/main/java/org/bytedeco/javacpp/opencv_imgproc.java | sed -E 's/^[ ]*//g' | tr '\n' '`' | sed 's/,`/, /g' | tr '`' '\n' | grep '^@Namespace' | awk '-F,' '{print NF}' | sort --unique -n
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# 6
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# 7
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# 8
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# 10
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def test_opencv_calc_hist4():
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src_image = opencv_core.Mat([128, 128])
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src_images = opencv_core.MatVector()
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# print(dir(src_images))
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src_images.push_back(src_image)
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print(type(src_images))
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# <type 'org.bytedeco.javacpp.opencv_core$MatVector'>
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print(src_images)
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# [org.bytedeco.javacpp.opencv_core$Mat[width=1024,height=1024,depth=8,channels=3]]
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opencv_imgproc.calcHist(src_images, [0], None, None, [256], [0.0, 256.0])
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# TypeError: calcHist(): 1st arg can't be coerced to org.bytedeco.javacpp.opencv_core$UMatVector, org.bytedeco.javacpp.opencv_core$GpuMatVector, org.bytedeco.javacpp.opencv_core$MatVector
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def test_opencv_calc_hist5():
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src_image = opencv_core.Mat([128, 128])
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histogram = opencv_core.Mat()
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# @Namespace("cv") public static native void calcHist( @Const Mat images, int nimages, @Const int[] channels, @ByVal Mat mask, @ByVal Mat hist, int dims, @Const int[] histSize, @Const @ByPtrPtr float[] ranges );
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opencv_imgproc.calcHist(src_image, 1, [0], None, histogram, 1, [256], [0.0, 256.0])
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# at org.bytedeco.javacpp.opencv_imgproc.calcHist(Native Method)
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# at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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# at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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# at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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# at java.lang.reflect.Method.invoke(Method.java:497)
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# java.lang.NullPointerException: java.lang.NullPointerException: Pointer address of argument 3 is NULL.
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def test_opencv_calc_hist6():
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src_image = opencv_core.Mat([128, 128])
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histogram = opencv_core.Mat()
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mask = opencv_core.Mat()
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# @Namespace("cv") public static native void calcHist( @Const Mat images, int nimages, @Const int[] channels, @ByVal Mat mask, @ByVal Mat hist, int dims, @Const int[] histSize, @Const @ByPtrPtr float[] ranges );
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opencv_imgproc.calcHist(src_image, 1, [0], mask, histogram, 1, [256], [0.0, 256.0])
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# java.lang.RuntimeException: java.lang.RuntimeException: OpenCV(3.4.2) /Users/travis/build/bytedeco/javacpp-presets/opencv/cppbuild/macosx-x86_64/opencv-3.4.2/modules/imgproc/src/histogram.cpp:918: error: (-210:Unsupported format or combination of formats) in function 'calcHist'
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def test_opencv_calc_hist7():
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pixel_type=0
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# 0 : depth=8
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# 1 : depth=-2147483640
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# 2 : depth=16
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# 3 : depth=-2147483640
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# 4 : depth=-2147483640
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# 8 : depth=8, channels=2
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src_image = opencv_core.Mat().zeros(128, 128, pixel_type).asMat()
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print('src_image', src_image)
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histogram = opencv_core.Mat()
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print('histogram', histogram)
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mask = opencv_core.Mat()
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print('mask', mask)
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# @Namespace("cv") public static native void calcHist( @Const Mat images, int nimages, @Const int[] channels, @ByVal Mat mask, @ByVal Mat hist, int dims, @Const int[] histSize, @Const @ByPtrPtr float[] ranges );
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opencv_imgproc.calcHist(src_image, 1, [0], mask, histogram, 1, [256], [0.0, 256.0])
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def test_opencv():
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'''
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'''
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# https://forum.image.sc/t/use-opencv-within-jython-macro/10320/4
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test_opencv_calc_hist7()
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# histogram = opencv_imgproc.calcHist(images=[src_image], channels=[0], mask=None, histSize=[256], ranges=[0, 256])
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# histogram = opencv_imgproc.calcHist(src_image, 0, None, 3, [256], [0.0, 256.0], True, False)
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# print(dir(opencv_imgproc))
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# help(opencv_imgproc.cvCalcHist)
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# opencv_imgproc.calcHist(src_image, None, histogram)
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# histogram = opencv_imgproc.cvCalcHist(src_image, None, [256], [0.0, 256.0])
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# import inspect
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# lines = inspect.getsource(opencv_imgproc.calcHist)
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# opencv_imgproc.calcHist(src_image, histogram)
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# there are 2 calcHist functions in /Applications/Fiji.app/jars/opencv-3.4.2-1.4.2.jar, and they take 6 or 7 arguments :
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# jar -xvf /Applications/Fiji.app/jars/opencv-3.4.2-1.4.2.jar
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# [1]graffy@pr079234:~/toto/jython[15:18:17]>javap ./org/opencv/imgproc/Imgproc.class | grep calcHist
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# public static void calcHist(java.util.List<org.opencv.core.Mat>, org.opencv.core.MatOfInt, org.opencv.core.Mat, org.opencv.core.Mat, org.opencv.core.MatOfInt, org.opencv.core.MatOfFloat, boolean);
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# public static void calcHist(java.util.List<org.opencv.core.Mat>, org.opencv.core.MatOfInt, org.opencv.core.Mat, org.opencv.core.Mat, org.opencv.core.MatOfInt, org.opencv.core.MatOfFloat);
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#
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# jar -xvf /Applications/Fiji.app/jars/opencv-3.4.2-1.4.2-macosx-x86_64.jar
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# [OK]graffy@pr079234:~/toto/jython[19:02:28]>grep -A 5 "calcHist(" org/bytedeco/javacpp/macosx-x86_64/include/opencv2/imgproc.hpp
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# CV_EXPORTS void calcHist( const Mat* images, int nimages,
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# const int* channels, InputArray mask,
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# OutputArray hist, int dims, const int* histSize,
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# const float** ranges, bool uniform = true, bool accumulate = false );
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# /** @overload
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# --
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# CV_EXPORTS void calcHist( const Mat* images, int nimages,
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# const int* channels, InputArray mask,
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# SparseMat& hist, int dims,
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# const int* histSize, const float** ranges,
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# bool uniform = true, bool accumulate = false );
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# --
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# CV_EXPORTS_W void calcHist( InputArrayOfArrays images,
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# const std::vector<int>& channels,
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# InputArray mask, OutputArray hist,
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# const std::vector<int>& histSize,
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# const std::vector<float>& ranges,
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# bool accumulate = false );
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# git checkout tags/1.4.2
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# [OK]graffy@pr079234:~/toto/javacpp-presets[19:21:57]>git branch
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# * (HEAD detached at 1.4.2)
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# [OK]graffy@pr079234:~/toto/javacpp-presets[19:18:33]>grep -A 2 "void cvCalcHist" ./opencv/src/main/java/org/bytedeco/javacpp/opencv_imgproc.java
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# public static native void cvCalcHist( @Cast("IplImage**") PointerPointer image, CvHistogram hist,
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# int accumulate/*=0*/,
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# @Const CvArr mask/*=NULL*/ );
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# --
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# public static native void cvCalcHist( @ByPtrPtr IplImage image, CvHistogram hist );
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# public static native void cvCalcHist( @ByPtrPtr IplImage image, CvHistogram hist,
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# int accumulate/*=0*/,
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# @Const CvArr mask/*=NULL*/ );
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# [OK]graffy@pr079234:~/toto/javacpp-presets[19:18:41]>grep -A 2 "void cvCalcHist" ./opencv/src/main/java/org/bytedeco/javacpp/helper/opencv_imgproc.java
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# public static void cvCalcHist(IplImage[] arr, CvHistogram hist, int accumulate/*=0*/, CvArr mask/*=null*/) {
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# org.bytedeco.javacpp.opencv_imgproc.cvCalcHist(new IplImageArray(arr), hist, accumulate, mask);
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# }
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# --
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# public static void cvCalcHist(IplImageArray arr, CvHistogram hist,
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# int accumulate/*=0*/, CvArr mask/*=null*/) {
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# org.bytedeco.javacpp.opencv_imgproc.cvCalcArrHist(arr, hist, accumulate, mask);
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def get_image_median_value(src_image):
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return 0
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def test_get_image_median_value():
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image_file_path = '/Users/graffy/ownCloud/ipr/lipase/raw-images/res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/img_000000000_DM300_327-353_fluo_000.tif'
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image = imread(image_file_path)
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median_value = get_image_median_value(image)
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print('median value : %d' % median_value)
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# double median( cv::Mat channel )
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# {
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# double m = (channel.rows*channel.cols) / 2;
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# int bin = 0;
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# double med = -1.0;
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# int histSize = 256;
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# float range[] = { 0, 256 };
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# const float* histRange = { range };
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# bool uniform = true;
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# bool accumulate = false;
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# cv::Mat hist;
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# cv::calcHist( &channel, 1, 0, cv::Mat(), hist, 1, &histSize, &histRange, uniform, accumulate );
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# for ( int i = 0; i < histSize && med < 0.0; ++i )
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# {
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# bin += cvRound( hist.at< float >( i ) );
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# if ( bin > m && med < 0.0 )
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# med = i;
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# }
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# return med;
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# }
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def find_depth_index(src_image, white_sequence):
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''' finds in the image sequence white_sequence the image that correlates the best to src_image
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:param cv_core.Mat src_image:
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:param Sequence white_sequence:
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'''
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for z_index in range(white_sequence.num_slices):
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white_image_file_path = white_sequence.get_image_file_path(channel_index=0, frame_index=0, z_index=z_index)
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# white_image = IJ.openImage(white_image_file_path)
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# imp2mat = ImagePlusMatConverter()
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# white_mat = imp2mat.toMat(white_image.getProcessor())
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white_mat = imread(white_image_file_path)
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print white_mat
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break
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def process_sequence(sequence):
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'''
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:param Sequence sequence:
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'''
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white_seq = sequence.get_white()
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src_image_file_path = sequence.get_image_file_path(channel_index=0, frame_index=0, z_index=0)
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src_image = imread(src_image_file_path)
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# src_image = IJ.openImage(src_image_file_path)
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find_depth_index(src_image, white_seq)
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def run_script():
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raw_images_root = '/Users/graffy/ownCloud/ipr/lipase/raw-images'
|
||||
catalog = ImageCatalog(raw_images_root)
|
||||
print(catalog)
|
||||
# catalog.sequences['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0'].open_in_imagej()
|
||||
catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2'].open_in_imagej()
|
||||
# catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2'].open_in_imagej()
|
||||
# catalog.sequences['DARK_40X_60min_1 im pae min_1/Pos0'].open_in_imagej()
|
||||
# catalog.sequences['white_24112018_1/Pos0'].open_in_imagej()
|
||||
process_sequence(catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2'])
|
||||
|
||||
if False:
|
||||
sequence = catalog.sequences['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
|
||||
src_image_file_path = sequence.get_image_file_path(channel_index=sequence.get_channel_index('DM300_327-353_fluo'), frame_index=3)
|
||||
src_image = IJ.openImage(src_image_file_path)
|
||||
src_image = IJ.openImage(src_image_file_path) # pylint: disable=unused-variable
|
||||
|
||||
# dark_image = IJ.openImage(raw_images_root + '/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/img_000000000_DM300_327-353_fluo_000.tif')
|
||||
# src_image.show()
|
||||
# assert src_image
|
||||
|
||||
|
||||
# If a Jython script is run, the variable __name__ contains the string '__main__'.
|
||||
# If a script is loaded as module, __name__ has a different value.
|
||||
if __name__ in ['__builtin__', '__main__']:
|
||||
run_script()
|
||||
# run_script()
|
||||
# test_get_image_median_value()
|
||||
test_opencv()
|
||||
|
|
|
|||
Loading…
Reference in New Issue