97 lines
3.8 KiB
Python
97 lines
3.8 KiB
Python
import os
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import pickle
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from PIL import Image
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from stack3d.study.components import StudyData, MouseData, TimepointData
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def get_time(path):
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no_space = path.replace(" ", "")
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day_index = no_space.find("Day")
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day_string = no_space[day_index+3:day_index+5]
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day_string = day_string.replace("_", "")
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return int(day_string)
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def merge_plots(work_dir, study_collection):
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plot_name = "diameterPlot"
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plot_name = "histogramDiameter"
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plot_name = "rendering"
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reduction_factor = 1
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reduction_factor2 = 1
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for eachStudy in study_collection:
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print "Merging Study: ", eachStudy.raw_data_path
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study_dir = work_dir + "/" + eachStudy.raw_data_path
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merge_paths = []
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for eachMouse in eachStudy.mice:
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print "Merging Mouse: ", eachMouse.raw_data_path
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mouse_dir = study_dir + "/" + eachMouse.raw_data_path
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image_paths = []
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# first sort time points
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days = []
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for eachTimePoint in eachMouse.timepoints:
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days.append(get_time(eachTimePoint.raw_data_path))
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if len(days) > 0:
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days, eachMouse.timepoints = (list(t) for t in zip(*sorted(zip(days, eachMouse.timepoints))))
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for eachTimePoint in eachMouse.timepoints:
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time_dir = mouse_dir + "/" + eachTimePoint.raw_data_path
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#base_path = "/analysis_analysis/plots/vessels/" + plot_name + ".png"
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base_path = "/analysis_analysis/histograms/" + plot_name + ".png"
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base_path = "/analysis_analysis//" + plot_name + ".tiff"
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if os.path.isfile(time_dir + base_path):
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image_paths.append(time_dir + base_path)
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merge_path = mouse_dir + "/timeline_" + plot_name + ".jpg"
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merge_axis = 0
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print "Merging plots to: ", merge_path
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if len(image_paths) > 0:
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widths = []
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heights = []
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for path in image_paths:
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im = Image.open(path)
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widths.append(im.size[0])
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heights.append(im.size[1])
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im.close()
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total_width = int(0.5*sum(widths))
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max_height = int(0.8*max(heights))
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new_im = Image.new('RGB', (total_width, max_height))
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x_offset = 0
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for path in image_paths:
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im = Image.open(path)
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img2 = im.crop((int(0.25*im.size[0]), int(0.2*im.size[1]), int(0.75*im.size[0]), im.size[1]))
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new_im.paste(img2, (x_offset, 0))
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x_offset += int(0.5*im.size[0])
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im.close()
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new_im.thumbnail((total_width/reduction_factor, max_height/reduction_factor))
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merge_paths.append(merge_path)
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new_im.save(merge_path)
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if len(merge_paths) > 0:
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widths = []
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heights = []
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for path in merge_paths:
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im = Image.open(path)
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widths.append(im.size[0])
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heights.append(im.size[1])
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im.close()
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max_width = max(widths)
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total_height = sum(heights)
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new_im = Image.new('RGB', (max_width, total_height))
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y_offset = 0
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for path in merge_paths:
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im = Image.open(path)
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new_im.paste(im, (0, y_offset))
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y_offset += im.size[1]
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im.close()
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new_im.thumbnail((max_width/reduction_factor2, total_height/reduction_factor2))
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new_im.save(study_dir + "/timeline_" + plot_name + ".jpg")
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work_dir = "/scratch/jgrogan/stack-working/study/"
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f = open(work_dir + "/study_collection.p", 'r')
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study_collection = pickle.load(f)
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merge_plots(work_dir, study_collection)
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