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New features: 1. Set default colors for elemental mappings 2. Plot all elements in the overlayed mapping by default
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| import argparse | ||
|
|
||
| def parse(): | ||
| parser = argparse.ArgumentParser(description = "Convert .emd file generated by Velox to images") | ||
|
|
||
| parser.add_argument ( | ||
| "-f", | ||
| "--file", | ||
| type = str, | ||
| metavar = "FILE", | ||
| help = "Input *.emd(Velox) filename (without \".emd\" extension)", | ||
| required=True | ||
| ) | ||
| parser.add_argument ( | ||
| "-o", | ||
| "--out", | ||
| type = str, | ||
| metavar = "TYPE", | ||
| help = "Type of output images.", | ||
| default = "png" | ||
| ) | ||
| parser.add_argument ( | ||
| "-ns", | ||
| "--no_scale", | ||
| help = "Do not draw scale bar", | ||
| action = "store_true" | ||
| ) | ||
| parser.add_argument ( | ||
| "-sc", | ||
| "--scale_color", | ||
| type = str, | ||
| metavar = "COLOR", | ||
| help = "Color of scale bar", | ||
| default = "#ffffff" | ||
| ) | ||
| parser.add_argument ( | ||
| "-s", | ||
| "--scale", | ||
| type = float, | ||
| nargs = 3, | ||
| metavar = "FLOAT", | ||
| help = "The position and width of scale bar (X_POSITION Y_POSITION WIDTH_FACTOR), the width is set as image-height/WIDTH_FACTOR", | ||
| default = [0.75, 0.9167, 150.0] | ||
| ) | ||
| parser.add_argument ( | ||
| "-e", | ||
| "--eds", | ||
| type = str, | ||
| nargs = "+", | ||
| metavar = "Str", | ||
| help = "The color of elemental mappings (default: gray)", | ||
| default = [] | ||
| ) | ||
| parser.add_argument ( | ||
| "-oe", | ||
| "--overlay", | ||
| type = str, | ||
| nargs = "+", | ||
| metavar = "ELEMENT", | ||
| help = "The elements for overlayed mapping", | ||
| default = [] | ||
| ) | ||
| parser.add_argument ( | ||
| "-oa", | ||
| "--overlay_alpha", | ||
| type = float, | ||
| metavar = "ALPHA", | ||
| help = "Transparency of the overlayed elemental mapping (a value between 0 and 1, 0 means totally transparent)", | ||
| default = "1.0" | ||
| ) | ||
| parser.add_argument ( | ||
| "-sa", | ||
| "--substrate_alpha", | ||
| type = float, | ||
| metavar = "ALPHA", | ||
| help = "Transparency of the HAADF substrate picture in elemental mapping (a value between 0 and 1, 0 means totally transparent)", | ||
| default = "0.5" | ||
| ) | ||
| parser.add_argument ( | ||
| "-c", | ||
| "--contrast_stretching", | ||
| type = float, | ||
| nargs = 2, | ||
| metavar = "CONTRAST", | ||
| help = "The parameter for contrast streaching, where the image is rescaled to include all intensities that fall within the given percentiles", | ||
| default = [1, 99] | ||
| ) | ||
|
|
||
| return parser |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
| import os | ||
| import matplotlib.pyplot as plt | ||
| import convert_emd.function as emdfun | ||
|
|
||
| def draw_scale_bar(frame, size_x, size_y, sb_x_start, sb_y_start, width_factor, sb_color): | ||
| sb_lst = [0.1,0.2,0.5,1,2,5,10,20,50,100,200,500,1000,2000,5000] | ||
| scale, unit = emdfun.get_scale(frame) | ||
| sb_len_float = size_x * scale / 6 | ||
| sb_len = sorted(sb_lst, key=lambda a: abs(a - sb_len_float))[0] | ||
| sb_len_px = sb_len / scale | ||
| sb_start_x, sb_start_y, sb_width = (size_x * sb_x_start , size_y * sb_y_start, size_y / width_factor) | ||
| return [plt.Rectangle((sb_start_x, sb_start_y), sb_len_px, sb_width, color=sb_color, fill=True), "_" + str(sb_len) + unit] | ||
|
|
||
| def convert_emd(file_name, data, output_type, scale_bar, sb_color, sb_x_start, sb_y_start, sb_width_factor, stretch, overlay_alpha, sub_alpha, eds_color, mapping_overlay, overlay): | ||
| output_dir = file_name + "/" | ||
| output_name = output_dir + file_name + "_" | ||
|
|
||
| if not os.path.exists(output_dir): | ||
| os.makedirs(output_dir) | ||
| mapping_frame = [] | ||
| ele = 0 | ||
| default_colors = emdfun.default_colors() | ||
|
|
||
| for i in range(len(data)): | ||
| frame = data[i] | ||
| dim = frame["data"].ndim | ||
| title = emdfun.get_title(frame) | ||
|
|
||
| if dim == 2: | ||
| frame["data"] = emdfun.contrast_stretch(frame, stretch) | ||
| cmp = "gray" | ||
| if overlay and not emdfun.is_eds_spectrum(frame): | ||
| if title in mapping_overlay: mapping_frame.append(i) | ||
| if title in eds_color: | ||
| cmp = emdfun.create_cmp(eds_color[title]) | ||
| elif title == "HAADF": | ||
| mapping_frame.append(i) | ||
| HAADF_frame_num = len(mapping_frame) - 1 | ||
| else: | ||
| cmp = emdfun.create_cmp(default_colors[ele]) | ||
| eds_color[title] = default_colors[ele] | ||
| ele += 1 | ||
| if ele > 9: ele = 0 | ||
|
|
||
| size_x, size_y = (frame["axes"][1]["size"], frame["axes"][0]["size"]) | ||
| plt.figure(figsize=(size_x/100, size_y/100), facecolor="black") | ||
| ax = plt.gca() | ||
| plt.imshow(frame["data"], cmap=cmp) | ||
|
|
||
| if scale_bar == True: | ||
| bar = draw_scale_bar(frame, size_x, size_y, sb_x_start, sb_y_start, sb_width_factor, sb_color) | ||
| ax.add_patch(bar[0]) | ||
| sb_text = bar[1] | ||
|
|
||
| plt.subplots_adjust(top=1, bottom=0, right=1, left=0, hspace=0, wspace=0) | ||
| plt.margins = (0, 0) | ||
| plt.axis("off") | ||
| if scale_bar == True: | ||
| plt.savefig(output_name + title + "_" + str(i) + sb_text + output_type) | ||
| else: | ||
| plt.savefig(output_name + title + "_" + str(i) + output_type) | ||
| plt.close() | ||
|
|
||
| if overlay: | ||
| element = "" | ||
| HAADF_frame = data[mapping_frame[HAADF_frame_num]] | ||
| size_x, size_y = (HAADF_frame["axes"][1]["size"], HAADF_frame["axes"][0]["size"]) | ||
|
|
||
| plt.figure(figsize=(size_x/100, size_y/100), facecolor="black") | ||
| ax = plt.gca() | ||
| plt.imshow(HAADF_frame["data"], cmap="gray", alpha=sub_alpha) | ||
| for i in range(len(mapping_frame)): | ||
| if i == HAADF_frame_num: | ||
| continue | ||
| title = emdfun.get_title(data[mapping_frame[i]]) | ||
| plt.imshow(data[mapping_frame[i]]["data"], cmap = emdfun.create_cmp(eds_color[title]), alpha = overlay_alpha) | ||
| element = element + "_" + title | ||
|
|
||
| if scale_bar == True: | ||
| bar = draw_scale_bar(HAADF_frame, size_x, size_y, sb_x_start, sb_y_start, sb_width_factor, sb_color) | ||
| ax.add_patch(bar[0]) | ||
| sb_text = bar[1] | ||
|
|
||
| plt.subplots_adjust(top=1, bottom=0, right=1, left=0, hspace=0, wspace=0) | ||
| plt.margins = (0, 0) | ||
| plt.axis("off") | ||
| if scale_bar == True: | ||
| plt.savefig(output_name + "Overlay" + element + sb_text + output_type) | ||
| else: | ||
| plt.savefig(output_name + "Overlay" + element + output_type) | ||
| plt.close() |
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