예제 #1
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파일: cmdtool.py 프로젝트: manerotoni/cecog
    def __init__(self, mapper, images):
        super(ImageProcessor, self).__init__()
        self.mapper = mapper
        self._channels = OrderedDict()

        self.metaimages = dict()
        for name, image in images.iteritems():
            metaimage = MetaImage()
            metaimage.set_image(ccore.readImage(image))
            self.metaimages[name] = [metaimage]

        self.mapper.setImageSize(metaimage.width, metaimage.height)
        self._setupChannels(images)
예제 #2
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    def __init__(self, mapper, images):
        super(ImageProcessor, self).__init__()
        self.mapper = mapper
        self._channels = OrderedDict()

        self.metaimages = dict()
        for name, image in images.iteritems():
            metaimage = MetaImage()
            metaimage.set_image(ccore.readImage(image))
            self.metaimages[name] = [metaimage]

        self.mapper.setImageSize(metaimage.width, metaimage.height)
        self._setupChannels(images)
예제 #3
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    def _run(self, meta_image):
        image = meta_image.image

        coords = dict(
            plate=meta_image.image_container.current_plate,
            pos=meta_image.coordinate.position,
            time=meta_image.coordinate.time,
            zslice=meta_image.coordinate.zslice,
            channel=meta_image.coordinate.channel,
        )

        main_folder = self.params['segmentation_folder']
        #FIXME: This is useful enought to put into an reusable function, maybe in utils?
        locator = self.params["loader_regex"] % coords
        locator_split = locator.split('/')
        locator_match = '/'
        for loc in locator_split[:-1]:
            try:
                match_candidates = os.listdir(main_folder + locator_match)
                if len(match_candidates) == 0:
                    raise RuntimeError
            except:
                raise RuntimeError('No files found in ' + main_folder +
                                   locator_match)
            match_results = [
                m.group() for l in match_candidates
                for m in [re.search(loc, l)] if m
            ]
            if len(match_results) != 1:
                raise RuntimeError('Could not match ' + match_candidates[0] +
                                   ' with ' + loc)
            locator_match += match_results[0] + '/'

        match_candidates = os.listdir(main_folder + locator_match)

        match_results = [
            m.group() for l in match_candidates
            for m in [re.search(locator_split[-1], l)] if m
        ]
        if len(match_results) == 0:
            raise RuntimeError('Could not match ', match_candidates[0], 'with',
                               locator_split[-1])

        match_result = match_results[0]

        img = ccore.readImage(main_folder + locator_match + match_result)
        #        img_pre = SegmentationPluginPrimary.prefilter(self, img, 2)
        #        img_bin = SegmentationPluginPrimary.threshold(self, img_pre, 20, 3)

        container = ccore.ImageMaskContainer(image, img, False)
        return container
예제 #4
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    def get_image(self, coordinate):
        index = 0
        zslice = coordinate.zslice
        if self.has_multi_images and self.multi_image == self.MULTIIMAGE_USE_ZSLICE:
            index = zslice - 1
            zslice = None

        filename_rel = self.dimension_lookup[coordinate.position][coordinate.time][coordinate.channel][zslice]
        filename_abs = os.path.join(self.path, filename_rel)
        # make sure no back-slashes are left in the path
        filename_abs = filename_abs.replace("\\", "/")
        if self.meta_data.pixel_type == PixelType.name(PixelType.Uint8):
            image = ccore.readImage(filename_abs, index)
        elif self.meta_data.pixel_type == PixelType.name(PixelType.Uint16):
            image = ccore.readImageUInt16(filename_abs, index)
        else:
            image = ccore.readImageUInt16(filename_abs, index)
        return image
예제 #5
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    def _run(self, meta_image):
        image = meta_image.image

        coords = dict(
            plate = meta_image.image_container.current_plate,
            pos = meta_image.coordinate.position,
            time = meta_image.coordinate.time,
            zslice = meta_image.coordinate.zslice,
            channel = meta_image.coordinate.channel,
            )

        main_folder = self.params['segmentation_folder']
        #FIXME: This is useful enought to put into an reusable function, maybe in utils?
        locator = self.params["loader_regex"] % coords
        locator_split = locator.split('/')
        locator_match = '/'
        for loc in locator_split[:-1]:
            try:
                match_candidates = os.listdir(main_folder + locator_match)
                if len(match_candidates) == 0:
                    raise RuntimeError
            except:
                raise RuntimeError('No files found in ' + main_folder + locator_match)
            match_results = [m.group() for l in match_candidates for m in [re.search(loc, l)] if m]
            if len(match_results) != 1:
                raise RuntimeError('Could not match ' + match_candidates[0] + ' with ' + loc)
            locator_match += match_results[0] + '/'

        match_candidates = os.listdir(main_folder + locator_match)

        match_results = [m.group() for l in match_candidates for m in [re.search(locator_split[-1], l)] if m]
        if len(match_results) == 0:
            raise RuntimeError('Could not match ', match_candidates[0], 'with', locator_split[-1])

        match_result = match_results[0]

        img = ccore.readImage(main_folder + locator_match + match_result)
#        img_pre = SegmentationPluginPrimary.prefilter(self, img, 2)
#        img_bin = SegmentationPluginPrimary.threshold(self, img_pre, 20, 3)

        container = ccore.ImageMaskContainer(image, img, False)
        return container
예제 #6
0
파일: importer.py 프로젝트: imcf/cecog
 def get_image(self, coordinate):
     index = 0
     zslice = coordinate.zslice
     if (self.has_multi_images
             and self.multi_image == self.MULTIIMAGE_USE_ZSLICE):
         index = zslice - 1
         zslice = None
     filename_rel = self.dimension_lookup[coordinate.position] \
                                         [coordinate.time] \
                                         [coordinate.channel] \
                                         [zslice]
     filename_abs = os.path.join(self.path, filename_rel)
     # make sure no back-slashes are left in the path
     filename_abs = filename_abs.replace('\\', '/')
     if self.meta_data.pixel_type == UINT8:
         image = ccore.readImage(filename_abs, index)
     elif self.meta_data.pixel_type == UINT16:
         image = ccore.readImageUInt16(filename_abs, index)
     else:
         image = ccore.readImageUInt16(filename_abs, index)
     return image