Add initial files.

image/processing/median.py

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+"""
+Median filter on chosen image
+"""
+
+import logging
+from code.image.tools import it_wrapper
+import code.image.settings
+
+if __name__ == "__main__":
+    
+    # Do setup
+    tool_name = "median"
+    work_dir, image_data = code.image.settings.do_setup(tool_name)
+    logger1 = logging.getLogger('processing.'+tool_name)
+
+    output_path = work_dir+"/median"
+    
+    logger1.info('Start Filtering Image at: ' + work_dir)
+    image_type = it_wrapper.default_image_type()
+    
+    input_path = work_dir + "/convert/itk_tile_0_2_6.tiff"
+    logger1.info("Reading the image: " +input_path + " into ITK")
+    reader = it_wrapper.read_image(input_path, image_type)
+    correct = it_wrapper.correct_spacing(reader, image_type, image_data["VoxelSizeZ"])
+            
+    logger1.info('Doing Median Filter')
+    median_filter = it_wrapper.median_filter(correct, image_type, 1)
+    
+    logger1.info('Writing TIFF Stack')
+    it_wrapper.write_image(output_path+"/itk_tile_0_2_6.tiff", image_type, median_filter)

image/processing/projection.py

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+"""
+SUM projection of tiled images
+"""
+
+import logging
+from code.image.tools import it_wrapper
+import code.image.settings
+
+if __name__ == "__main__":
+    
+    # Do setup
+    tool_name = "projection"
+    work_dir, image_data = code.image.settings.do_setup(tool_name)
+    logger1 = logging.getLogger('processing.'+tool_name)
+
+    output_path = work_dir+"/projection"
+    
+    logger1.info('Start Projecting Image at: ' + work_dir)
+    image_type = it_wrapper.default_image_type()
+    
+    num_tiles_y = 3
+    num_tiles_x = 3
+    for jdx in range(num_tiles_y):
+        for idx in range(num_tiles_x):
+            label = str(idx) + "_" + str(jdx) +"_"+ str(idx+ num_tiles_x*jdx)
+            input_path = work_dir + "/convert/itk_tile_" + label + ".tiff"
+            logger1.info("Reading the image: " +input_path + " into ITK")
+            reader = it_wrapper.read_image(input_path, image_type)
+            correct = it_wrapper.correct_spacing(reader, image_type, image_data["VoxelSizeZ"])
+            
+            logger1.info('Doing SUM projection')
+            project = it_wrapper.sum_projection(correct, image_type)
+    
+            output_image_type = it_wrapper.image_type_2d()
+            logger1.info('Writing TIFF Stack')
+            it_wrapper.write_image(output_path+"/sum_tile_" + label + ".tiff", output_image_type, project)

image/processing/reduce.py

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+"""
+Median filter on chosen image
+"""
+
+import logging
+from code.image.tools import it_wrapper
+import code.image.settings
+
+if __name__ == "__main__":
+    
+    # Do setup
+    tool_name = "reduce"
+    work_dir, image_data = code.image.settings.do_setup(tool_name)
+    logger1 = logging.getLogger('processing.'+tool_name)
+
+    output_path = work_dir+"/reduce"
+    
+    logger1.info('Start Reducing Image at: ' + work_dir)
+    image_type = it_wrapper.default_image_type()
+    
+    input_path = work_dir + "/median/itk_tile_0_2_6.tiff"
+    logger1.info("Reading the image: " +input_path + " into ITK")
+    reader = it_wrapper.read_image(input_path, image_type)
+    correct = it_wrapper.correct_spacing(reader, image_type, image_data["VoxelSizeZ"])
+            
+    logger1.info('Doing Reduction')
+    im_reduce = it_wrapper.shrink_image(image_type, correct, [2,2,1])
+    
+    logger1.info('Writing TIFF Stack')
+    it_wrapper.write_image(output_path+"/itk_tile_0_2_6.tiff", image_type, im_reduce)

image/processing/show.py

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+"""
+Show a tiff using vtk
+"""
+
+import code.image.settings
+from code.image.tools import simple_render
+from code.image.tools import it_wrapper
+
+work_dir, input_data = code.image.settings.do_setup("show")
+input_path = work_dir + "/threshold/itk_tile_0_2_6.tiff"
+
+image_type = it_wrapper.default_image_type()
+reader = it_wrapper.read_image(input_path, image_type)
+correct = it_wrapper.correct_spacing(reader, image_type, input_data["VoxelSizeZ"])
+converter = it_wrapper.convert_vtk(reader, image_type)
+    
+simple_render.render_image(converter, threshold = 1.0)

image/processing/threshold.py

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+"""
+Threshold on chosen image
+"""
+
+import logging
+from code.image.tools import it_wrapper
+import code.image.settings
+
+if __name__ == "__main__":
+    
+    # Do setup
+    tool_name = "threshold"
+    work_dir, image_data = code.image.settings.do_setup(tool_name)
+    logger1 = logging.getLogger('processing.'+tool_name)
+
+    output_path = work_dir+"/threshold"
+    
+    logger1.info('Start Thresholding Image at: ' + work_dir)
+    image_type = it_wrapper.default_image_type()
+    
+    input_path = work_dir + "/reduce/itk_tile_0_2_6.tiff"
+    logger1.info("Reading the image: " +input_path + " into ITK")
+    reader = it_wrapper.read_image(input_path, image_type)
+    correct = it_wrapper.correct_spacing(reader, image_type, image_data["VoxelSizeZ"])
+            
+    logger1.info('Doing Thresholding')
+    threshold = it_wrapper.threshold_image(image_type, correct, lower = 20, upper = 255)
+    
+    logger1.info('Writing TIFF Stack')
+    it_wrapper.write_image(output_path+"/itk_tile_0_2_6.tiff", image_type, threshold)

image/processing/tile.py

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+"""
+Merging of tiled images
+"""
+
+import logging
+from code.image.tools import it_wrapper
+import code.image.settings
+
+if __name__ == "__main__":
+    
+    # Do setup
+    tool_name = "tile"
+    work_dir, image_data = code.image.settings.do_setup(tool_name)
+    logger1 = logging.getLogger('processing.'+tool_name)
+
+    output_path = work_dir+"/projection"
+    
+    logger1.info('Start Merging Images at: ' + work_dir)
+    image_type = it_wrapper.default_image_type()
+    
+    num_tiles_y = 3
+    num_tiles_x = 3
+    container = []
+    for jdx in range(num_tiles_y):
+        for idx in range(num_tiles_x):
+            
+            label = str(idx) + "_" + str(jdx) +"_"+ str(idx+ num_tiles_x*jdx)
+            input_path = work_dir + "/projection/sum_tile_" + label + ".tiff"
+            logger1.info("Reading the image: " +input_path + " into ITK")
+            reader = it_wrapper.read_image(input_path, image_type)
+            correct = it_wrapper.correct_spacing(reader, image_type, image_data["VoxelSizeZ"])
+            container.append(correct)
+    
+    logger1.info('Merging Tiles')    
+    merged = it_wrapper.merge_tiles(container, image_type, num_tiles_x)
+      
+    output_image_type = it_wrapper.default_image_type()
+    logger1.info('Writing TIFF Stack')
+    it_wrapper.write_image(output_path+"/sum_merge.tiff", output_image_type, merged)