lipase/lipase.py

# String(label="Please enter your name",description="Name field") name
# OUTPUT String greeting

# A Jython script with parameters.
# It is the duty of the scripting framework to harvest
# the 'name' parameter from the user, and then display
# the 'greeting' output parameter, based on its type.
from ij import IJ  # pylint: disable=import-error
from ij import ImagePlus  # pylint: disable=import-error
from ij.process import ByteProcessor  # pylint: disable=import-error
from ij.process import ImageStatistics
from ij.plugin import ImageCalculator
from ij.plugin import ZProjector
from ij import WindowManager

# greeting = "Hello, " + name + "!"


# image prefix :
# AF
# blé : coupes de blé
# CA : coupe d'amande
# FE : feuille d'épinard
# GGH : globule gras humain
# CRF chloroplastes de feuille d'épinard
# OL : oléosome
# DARK : dark
# white :
#
# - cin1 : cinétique 1
#    phiG_40x_1 : cinétique avant et après injection enzyme gastrique
#    phiG_40x_Zstack20um_1 : stack
#     0mn : on commence à enregistrer et on attend 10mn (pour le bleaching) -> phiG_40x_1
#    10mn : debut injection phase gastrique (poussée)
#    13mn : la phase gastrique (le petit tuyau contient 20ul) arrive dans la cellule d'un coup (1 nanol)
#    15mn : on arrête l'injection
#    50mn : on fait un stack -> phiG_40x_Zstack20um_1
#    51mn : début d'injection phase intestinale (poussée) -> phiG_I_40x_1
#    x mn : on arrête l'injection
#    90mn : on fait un stack -> phiG_I_40x_Zstack20um_1
# - cin2 :  autre échantillon similaire à cin1
# - cond[5678] : condition non réalistes
import json


class Sequence(object):
    def __init__(self, catalog, sequence_id, micro_manager_metadata_file_path):
        self.catalog = catalog
        self.sequence_id = sequence_id
        self.micro_manager_metadata_file_path = micro_manager_metadata_file_path
        print(micro_manager_metadata_file_path)

        with open(micro_manager_metadata_file_path, "r") as mmm_file:
            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)

    @property
    def num_frames(self):
        summary = self.mmm['Summary']
        return int(summary['Frames'])

    @property
    def width(self):
        summary = self.mmm['Summary']
        return int(summary['Width'])

    @property
    def height(self):
        summary = self.mmm['Summary']
        return int(summary['Height'])

    @property
    def num_channels(self):
        summary = self.mmm['Summary']
        return int(summary['Channels'])

    @property
    def num_slices(self):
        summary = self.mmm['Summary']
        return int(summary['Slices'])

    @property
    def num_bits_per_pixels(self):
        summary = self.mmm['Summary']
        return int(summary['BitDepth'])

    def get_root_path(self):
        return '/'.join(self.micro_manager_metadata_file_path.split('/')[:-1])

    def get_image_file_path(self, channel_index, frame_index, z_index=0):
        '''
        :param int channel_index:
        :param int frame_index:
        :param int z_index:
        '''
        assert frame_index < self.num_frames
        assert channel_index < self.num_channels
        frame_info = self.mmm['FrameKey-%d-%d-%d' % (frame_index, channel_index, z_index)]
        rel_file_path = frame_info['FileName']
        return self.get_root_path() + '/' + rel_file_path

    def get_channel_index(self, channel_id):
        '''
        :param str channel_id:
        '''
        summary = self.mmm['Summary']
        channel_index = summary['ChNames'].index(channel_id)
        return channel_index

    def get_black(self):
        ''' returns the black sequence related to the the sequence self

        :return Sequence:
        '''
        seqid_to_black = {
            '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',
            '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',
        }
        white_sequence = seqid_to_black[self.sequence_id]
        return self.catalog.sequences[white_sequence]

    def get_white(self):
        ''' returns the white sequence related to the the sequence self

        :return Sequence:
        '''
        # assert fixme : res_soleil2018/white/white_24112018_2/Pos0 is visible
        seqid_to_white = {
            'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0': 'res_soleil2018/white/white_24112018_2/Pos0',
            'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2': 'res_soleil2018/white/white_24112018_2/Pos0',
        }
        white_sequence = seqid_to_white[self.sequence_id]
        return self.catalog.sequences[white_sequence]

    def as_hyperstack(self):
        hyperstack = IJ.createHyperStack(self.sequence_id, self.width, self.height, self.num_channels, self.num_slices, self.num_frames, self.num_bits_per_pixels)
        for channel_index in range(self.num_channels):
            for frame_index in range(self.num_frames):
                slice_index = 0
                src_image_file_path = self.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
                # print(src_image_file_path)
                src_image = IJ.openImage(src_image_file_path)
                # print(src_image.getProperties())
                hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
                hyperstack.setProcessor(src_image.getProcessor())
        return hyperstack

    def as_stack(self, channel_id):
        '''
        :param str channel_id: eg 'DM300_327-353_fluo'
        '''
        channel_index = self.get_channel_index(channel_id)
        hyperstack = IJ.createHyperStack(self.sequence_id, self.width, self.height, 1, self.num_slices, self.num_frames, self.num_bits_per_pixels)
        for frame_index in range(self.num_frames):
            slice_index = 0
            src_image_file_path = self.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
            # print(src_image_file_path)
            src_image = IJ.openImage(src_image_file_path)
            # print(src_image.getProperties())
            hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
            hyperstack.setProcessor(src_image.getProcessor())
        return hyperstack

    def open_in_imagej(self):
        # ip = IJ.createHyperStack(title=self.sequence_id, width=self.width, height= self.height, channels=1, slices=1, frames=self.get_num_frames(), bitdepth=16)
        hyperstack = self.as_hyperstack()
        hyperstack.show()
        for channel_index in range(self.num_channels):
            hyperstack.setPositionWithoutUpdate(channel_index + 1, 1, 1)
            IJ.run("Enhance Contrast", "saturated=0.35")
        return hyperstack


class ImageCatalog(object):
    def __init__(self, raw_images_root):
        self.raw_images_root = raw_images_root
        self.sequences = {}

        # nb : we use the path as sequence id because the "Comment" field in the summary section of the metadata file is not guaranteed to be unique (eg they are the same in res_soleil2018/white/white_24112018_1/Pos0 and in res_soleil2018/white/white_24112018_2/Pos0)
        sequence_ids = []
        sequence_ids.append('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0')
        sequence_ids.append('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2')

        sequence_ids.append('res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0')
        sequence_ids.append('res_soleil2018/DARK/DARK_40X_zstack_vis_327-353_1/Pos0')

        # 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)
        sequence_ids.append('res_soleil2018/white/white_24112018_2/Pos0')

        for sequence_id in sequence_ids:
            micro_manager_metadata_file_path = raw_images_root + '/' + sequence_id + '/metadata.txt'
            # micro_manager_metadata_file_path = '/tmp/toto.json'
            self.sequences[sequence_id] = Sequence(self, sequence_id, micro_manager_metadata_file_path)

    def __str__(self):
        for sequence_id, sequence in self.sequences.iteritems():
            return str(sequence_id) + ':' + str(sequence)
        # self.add_micromanager_metadata(raw_images_root + '/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/metadata.txt')

    # def add_micromanager_metadata(self, micro_manager_metadata_file_path):
    #    self.sequences[ micro_manager_metadata_file_path ] = Sequence(self, micro_manager_metadata_file_path)


class IImageProcessingDebugger(object):

    def __init__(self):
        pass

    def on_image(self, image, image_id):
        '''
        :param ImagePlus image:
        :param str image_id:
        '''
        pass


class NullDebugger(IImageProcessingDebugger):

    def __init__(self):
        IImageProcessingDebugger.__init__(self)

    def on_image(self, image, image_id):
        pass


class ImageLogger(IImageProcessingDebugger):

    def __init__(self):
        IImageProcessingDebugger.__init__(self)

    def on_image(self, image, image_id):
        # todo : WindowManager
        image.show()


class Lipase(object):

    def __init__(self, debugger=NullDebugger()):
        '''
        :param IImageProcessingDebugger im_proc_debugger:
        '''
        self.debugger = debugger
        raw_images_root = '/Users/graffy/ownCloud/ipr/lipase/raw-images'
        self.catalog = ImageCatalog(raw_images_root)
        print(self.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['DARK_40X_60min_1 im pae min_1/Pos0'].open_in_imagej()
        # catalog.sequences['white_24112018_1/Pos0'].open_in_imagej()

    def get_image_median_value(self, src_image):
        '''
        :param ImagePlus src_image:
        '''
        # https://imagej.nih.gov/ij/developer/api/ij/process/ImageStatistics.html
        stats = ImageStatistics.getStatistics(src_image.getProcessor(), ImageStatistics.MEDIAN, None)
        # print(stats)
        # print(stats.pixelCount)
        return stats.median

    def get_image_mean_value(self, src_image):
        '''
        :param ImagePlus src_image:
        '''
        # https://imagej.nih.gov/ij/developer/api/ij/process/ImageStatistics.html
        stats = ImageStatistics.getStatistics(src_image.getProcessor(), ImageStatistics.MEAN, None)
        # print(stats)
        # print(stats.pixelCount)
        return stats.mean

    def test_get_image_median_value(self):
        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'
        image = IJ.openImage(image_file_path)
        median_value = self.get_image_median_value(image)
        print('median value : %d' % median_value)

    def find_depth_index(self, src_image, white_sequence):
        ''' finds in the image sequence white_sequence the image that correlates the best to src_image

        :param ImagePlus src_image:
        :param Sequence white_sequence:
        '''
        self.debugger.on_image(src_image, 'src_image')

        white_sequence.open_in_imagej()

        print('image type : ', src_image.getType())
        src_median_value = self.get_image_median_value(src_image)
        normalized_src_processor = src_image.getProcessor().convertToFloat()
        normalized_src_processor.multiply(1.0 / src_median_value)
        best_diff = None
        best_z_index = None
        for z_index in range(white_sequence.num_slices):
            white_image_file_path = white_sequence.get_image_file_path(channel_index=0, frame_index=0, z_index=z_index)
            white_image = IJ.openImage(white_image_file_path)
            # self.debugger.on_image(white_image, 'white_image')
            white_median_value = self.get_image_median_value(white_image)
            # white_to_src_factor = 1.0 / float(white_median_value)
            normalized_white_processor = white_image.getProcessor().convertToFloat()
            normalized_white_processor.multiply(1.0 / float(white_median_value))

            normalized_src = ImagePlus()  # IJ.openImage("http://imagej.nih.gov/ij/images/boats.gif")
            normalized_src.setProcessor(normalized_src_processor)
            # print(imp1)
            normalized_white = ImagePlus()  # IJ.openImage("http://imagej.nih.gov/ij/images/bridge.gif")
            normalized_white.setProcessor(normalized_white_processor)
            # print(imp2)
            ic = ImageCalculator()
            difference_image = ic.run("sub create float", normalized_src, normalized_white)
            # self.debugger.on_image(imp3, 'diff')

            # self.debugger.on_image(normalized_white, 'normalized_white')
            # self.debugger.on_image(difference_image, 'difference_image')

            # imp2mat = ImagePlusMatConverter()
            # white_mat = imp2mat.toMat(white_image.getProcessor())
            # white_mat = imread(white_image_file_path)
            # print(white_image)
            sqdiff_image = ic.run("mul create float", difference_image, difference_image)
            mean_sqdiff = self.get_image_mean_value(sqdiff_image)
            print('difference : ', mean_sqdiff)
            if best_diff is None or mean_sqdiff < best_diff:
                best_diff = mean_sqdiff
                best_z_index = z_index
        return best_z_index

    def compute_sequence_median_image(self, sequence, channel_id='DM300_nofilter_vis'):
        ''' computes for each pixel its median value along time, so that in the end we have a single image that only shows structures (things that don't move such as the traps)

        :param Sequence sequence:
        :param str channel_id:
        '''
        stack = sequence.as_stack(channel_id)
        projector = ZProjector()
        median_image = projector.run(stack, 'median')
        # pixel_value_along_time = ByteProcessor.createProcessor(stack.getDepth(), 1)
        return median_image

    def extract_background(self, sequence):
        channel_id = 'DM300_nofilter_vis'
        sequence.as_stack(channel_id).show()
        background_image = self.compute_sequence_median_image(sequence, channel_id)
        background_image.show()
        return background_image

    def process_sequence(self, sequence_id):
        '''
        :param str sequence_id:
        '''
        raise NotImplementedError()


def test_find_white():
    lipase = Lipase(debugger=ImageLogger())
    sequence = lipase.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2']
    white_seq = sequence.get_white()
    channel_index = sequence.get_channel_index('DM300_327-353_fluo')
    src_image_file_path = sequence.get_image_file_path(channel_index=channel_index, frame_index=0, z_index=0)
    src_image = IJ.openImage(src_image_file_path)
    # src_image = IJ.openImage(src_image_file_path)
    depth_index = lipase.find_depth_index(src_image, white_seq)


def run_script():
    test_find_white()

    if False:
        lipase = Lipase(debugger=ImageLogger())
        lipase.process_sequence('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2')

    if False:
        sequence = lipase.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)  # 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()
    # test_get_image_median_value()