preprocess_sequence plugin : added the ablilty to smooth the dark image to avoid infinite pixel values in the result
infinite pixel values happen when a pixel in the dark image has the same value as its counterpart in the white image (in a dark area, this can happen)
This commit is contained in:
Guillaume Raffy
parent
e397e3aa0f
commit
ae6de7ffef
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@ -1,10 +1,22 @@
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#@ String (choices={"no smooth", "gaussian blur"}, style="listBox", value="gaussian blur") DARK_SMOOTH_METHOD
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#@ Float (label="dark image gaussian blur sigma", style="slider", min=0.0, max=10.0, stepSize=0.1, value=3.0) DARK_GAUSSIAN_BLUR_SIGMA
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#@ ImagePlus (label="the input image stack") INPUT_STACK
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#@ ImagePlus (label="the input white image") INPUT_WHITE
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#@ ImagePlus (label="the input dark image") INPUT_DARK
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#@output ImagePlus PREPROCESSED_STACK
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# failed attempt to use alternative input parameters for headless testing but visibility=INVISIBLE doesn't make their widget disappear, unfortunately (see https://imagej.net/Script_parameters.html#Default_values)
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## String (label="the input image stack", visibility=INVISIBLE) INPUT_STACK_FILE
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## String (label="the input white image", visibility=INVISIBLE) INPUT_WHITE_FILE
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## String (label="the input dark image", visibility=INVISIBLE) INPUT_DARK_FILE
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"""This script is supposed to be launched from fiji's jython interpreter
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"""
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# to use log.info (see 3d_analytics_CH.py sample)
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#@LogService log
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#from ij import IJ # pylint: disable=import-error
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#WHITE_ESTIMATE = IJ.openImage('/Users/graffy/ownCloud/ipr/lipase/lipase.git/white_estimate.tiff')
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@ -32,17 +44,9 @@ from lipase.catalog import ImageCatalog
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from ij import IJ
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from ij.gui import GenericDialog, DialogListener
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from ij.plugin.filter import GaussianBlur
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from java.awt.event import ItemListener
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# class MyListener(DialogListener):
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# def dialogItemChanged(self, gd, event):
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# IJ.log("Something was changed (event = %s)" % event)
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# IJ.log("event's attributes : %s" % str(dir(event)))
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# # Something was changed (event = java.awt.event.ItemEvent[ITEM_STATE_CHANGED,item=res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0,stateChange=SELECTED] on choice0)
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# # event's attributes : ['ACTION_EVENT_MASK', 'ADJUSTMENT_EVENT_MASK', 'COMPONENT_EVENT_MASK', 'CONTAINER_EVENT_MASK', 'DESELECTED', 'FOCUS_EVENT_MASK', 'HIERARCHY_BOUNDS_EVENT_MASK', 'HIERARCHY_EVENT_MASK', 'ID', 'INPUT_METHOD_EVENT_MASK', 'INVOCATION_EVENT_MASK', 'ITEM_EVENT_MASK', 'ITEM_FIRST', 'ITEM_LAST', 'ITEM_STATE_CHANGED', 'KEY_EVENT_MASK', 'MOUSE_EVENT_MASK', 'MOUSE_MOTION_EVENT_MASK', 'MOUSE_WHEEL_EVENT_MASK', 'PAINT_EVENT_MASK', 'RESERVED_ID_MAX', 'SELECTED', 'TEXT_EVENT_MASK', 'WINDOW_EVENT_MASK', 'WINDOW_FOCUS_EVENT_MASK', 'WINDOW_STATE_EVENT_MASK', '__class__', '__copy__', '__deepcopy__', '__delattr__', '__doc__', '__ensure_finalizer__', '__eq__', '__format__', '__getattribute__', '__hash__', '__init__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__str__', '__subclasshook__', '__unicode__', 'class', 'equals', 'getClass', 'getID', 'getItem', 'getItemSelectable', 'getSource', 'getStateChange', 'hashCode', 'item', 'itemSelectable', 'notify', 'notifyAll', 'paramString', 'setSource', 'source', 'stateChange', 'toString', 'wait']
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def run_script():
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user_settings = UserSettings()
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@ -63,19 +67,26 @@ def run_script():
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if src_dark.get_pixel_type() != PixelType.F32:
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src_dark = src_dark.clone(clone_pixel_type=PixelType.F32)
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global DARK_SMOOTH_METHOD
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global DARK_GAUSSIAN_BLUR_SIGMA
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log.info('DARK_SMOOTH_METHOD=%s' % DARK_SMOOTH_METHOD)
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if DARK_SMOOTH_METHOD == 'gaussian blur':
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log.info('smoothing dark image with gaussian blur filter (sigma=%f)' % DARK_GAUSSIAN_BLUR_SIGMA)
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# ij.plugin.filter.GaussianBlur
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# blurGaussian
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gaussian_blur = GaussianBlur()
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accuracy = 0.0002 # comes from https://imagej.nih.gov/ij/developer/source/ij/plugin/filter/GaussianBlur.java.html
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gaussian_blur.blurFloat(src_dark.ij_image.getProcessor(), DARK_GAUSSIAN_BLUR_SIGMA, DARK_GAUSSIAN_BLUR_SIGMA, accuracy)
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dst_preproc_stack = IImageEngine.get_instance().create_hyperstack(width=src_hyperstack.get_width(), height=src_hyperstack.get_height(), num_channels=src_hyperstack.num_channels(), num_slices=src_hyperstack.num_slices(), num_frames=src_hyperstack.num_frames(), pixel_type=PixelType.F32)
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src_image_feeder = StackImageFeeder(src_hyperstack)
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# dst_image_feeder = StackImageFeeder(dst_preproc_stack)
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src_it = iter(src_image_feeder)
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# dst_it = iter(dst_image_feeder)
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frame_index = 0
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for src_image in src_it:
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nomin_image = ie.subtract(src_image, src_dark)
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denom_image = ie.subtract(src_white, src_dark)
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# preproc_image = IImageEngine.get_instance().create_image(width=src_hyperstack.get_width(), height=src_hyperstack.get_height(), pixel_type=PixelType.F32)
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# preproc_image = dst_it.next()
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preproc_image = ie.divide(nomin_image, denom_image)
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dst_preproc_stack.set_image(preproc_image, frame_index=frame_index, slice_index=0, channel_index=0) # TODO: use frame_index, slice_index and channel_index from feeder
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frame_index += 1
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