generate mask avoid real signal

cli/32bit_to8.py

+#!/usr/bin/env python
+# -*- coding:utf-8 -*-
+
+import os
+import cv2 as cv
+import argparse
+
+
+def get_args():
+    parser = argparse.ArgumentParser(description = 'Identify targets from background by KMeans or Threshold',
+                                     formatter_class = argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('-i', '--input', metavar = 'I', type = str, default = './',
+                        help = 'input_dir', dest = 'input')
+    parser.add_argument('-o','--output',metavar = 'O',type = str,default = './out/',help='output dir',dest = 'output')
+
+    return parser.parse_args()
+
+args = get_args()
+os.mkdir(args.output)
+
+for name in os.listdir(args.input):
+    img = cv.imread(args.input+name,flags = cv.IMREAD_GRAYSCALE)
+    cv.imwrite(args.output+name,img)
\ No newline at end of file

cvBasedMethod/util.py

@@ -4,8 +4,10 @@ import numpy as np
 import cv2 as cv
 import pandas as pd
 import matplotlib.pyplot as plt
+import seaborn as sns
 import logging
 import os
+import re
 from cvBasedMethod.filters import fft_mask,butterworth
 
 def remove_scratch(img):
@@ -71,32 +73,47 @@ def save_img(img_list, dir, name):
         plt.title(title)
         plt.imshow(img, 'gray')
     try:
-        os.makedirs('out/' + dir + '/graph')
+        os.makedirs('data/output/' + dir + '/graph')
     except:
-        logging.info('Existing dir: out/' + dir + '/graph')
-    plt.savefig('out/' + dir + '/graph/' + name + '.png')
+        logging.info('Existing dir: data/output/' + dir )
+    plt.savefig('data/output/' + dir + '/graph/' + name[:-4] + '.png')
     plt.close()
 
 
-def calcRes(img, mask, dir = 'output', name = 'output'):
+def calcRes(img, mask, dir = 'default_output', name = 'output'):
     dic = get_subarea_infor(img, mask)
     df = pd.DataFrame(dic)
     try:
-        os.makedirs('out/' + dir + '/csv')
+        os.makedirs('data/output/' + dir + '/csv')
     except:
         logging.info('Existing dir: out/' + dir + '/csv')
-    df.to_csv('out/' + dir + '/csv/' + name + '.csv')
+    if len(df)!=0:
+        df.to_csv('data/output/' + dir + '/csv/' + name + '.csv',index = False)
+
+
+def draw_bar(exName,names):
+    df = pd.DataFrame(columns = ('class', 'perc', 'Label', 'Area', 'Mean', 'Std', 'BackMean', 'BackStd'))
+    for name in names:
+        tmp = pd.read_csv('data/output/' + exName + '/csv/' + name)
+        match_group = re.match('.*\s([dD]2[oO]|[lL][bB]|.*ug).*\s(.+)\.csv', name)
+        tmp['perc'] = str.lower(match_group.group(1))[:-2] if str.lower(match_group.group(1)).endswith('ug') else str.lower(
+            match_group.group(1))
+        tmp['perc'].replace({'d2o':'0'},inplace = True)
+        tmp['class'] = str.lower(match_group.group(2))
+        df = df.append(tmp, ignore_index = True, sort = True)
+
+    df = df[df['Area']>19]
+    df['Pure'] = df['Mean'] - df['BackMean']
+
+    sns.set_style("darkgrid")
+    #sns.catplot(x = 'perc',y = 'Mean',hue = 'class',kind='bar',data = df)
+    sns.pairplot(df, vars = ['Area', 'Mean', 'perc','class'])
+    plt.show()
 
 
 def get_subarea_infor(img, mask):
     area_num, labels, stats, centroids = cv.connectedComponentsWithStats(mask)
-
-    label_group = []
-    area_group = []
-    mean_group = []
-    std_group = []
-    back_mean = []
-    back_std = []
+    info = []
 
     for i in filter(lambda x: x != 0, range(area_num)):
         group = np.where(labels == i)
@@ -113,19 +130,16 @@ def get_subarea_infor(img, mask):
                     res[x, y] = mask[x, y]
                 else:
                     res[x, y] = 0
+
         kernel = np.ones((17, 17), np.uint8)
         mask_background = cv.erode(255 - res, kernel)
         minimask = cv.bitwise_xor(mask_background, 255 - res)
+        realminimask = cv.bitwise_and(minimask, 255 - mask)
 
-        img_background = img[np.where(minimask != 0)]
+        img_background = img[np.where(realminimask != 0)]
         mean_value = np.mean(img_background)
         std_value = np.std(img_background)
 
-        label_group.append(i)
-        area_group.append(area_tmp)
-        mean_group.append(mean_tmp)
-        std_group.append(std_tmp)
+        info.append({'Label': i, 'Area': area_tmp, 'Mean': mean_tmp, 'Std': std_tmp, 'BackMean': mean_value,
+            'BackStd': std_value})
+    return info
\ No newline at end of file
-        back_mean.append(mean_value)
-        back_std.append(std_value)
-    return {'Label': label_group, 'Area': area_group, 'Mean': mean_group, 'Std': std_group, 'BackMean': back_mean,
-            'BackStd': back_std}

main.py

@@ -24,7 +24,7 @@ def method_threshold(imglist, process = 8):
 
 def method_newThreshold(imglist, process = 8):
     pool = Pool(process)
-    pool.map(lambda x: threshold(x,'fft'), imglist)
+    pool.map(lambda x: threshold(x, 'fft'), imglist)
     pool.close()
     pool.join()
 
@@ -32,8 +32,9 @@ def method_newThreshold(imglist, process = 8):
 def get_args():
     parser = argparse.ArgumentParser(description = 'Identify targets from background by KMeans or Threshold',
                                      formatter_class = argparse.ArgumentDefaultsHelpFormatter)
-    parser.add_argument('-m', '--method', metavar = 'M', type = int, default = 0,
-                        help = '0 for KMeans; 1 for Threshold; 2 for newThreshold', dest = 'method')
+    parser.add_argument('-m', '--method', metavar = 'M', type = int, default = 3,
+                        help = '0 for KMeans; 1 for Threshold; 2 for newThreshold; 3 for Unet; 4 for further process',
+                        dest = 'method')
     parser.add_argument('-c', '--core', metavar = 'C', type = int, default = 5, help = 'Num of cluster', dest = 'core')
     parser.add_argument('-p', '--process', metavar = 'P', type = int, default = 8, help = 'Num of process',
                         dest = 'process')
@@ -48,16 +49,18 @@ def get_args():
     return parser.parse_args()
 
 
-
-
 if __name__ == '__main__':
     args = get_args()
-    path = ['data/imgs/'+x for x in os.listdir('data/imgs')]
+    path = [(y, x) for y in filter(lambda x: x != '.DS_Store', os.listdir('data/imgs')) for x in filter(
+        lambda x: x.endswith('.tif') and not x.endswith('dc.tif') and not x.endswith('DC.tif') and not x.endswith(
+            'dc .tif'), os.listdir('data/imgs/' + y))]
     if args.method == 0:
-        method_kmeans(path,args.core)
+        method_kmeans(path, args.core)
     elif args.method == 1:
-        method_threshold(path,args.process)
+        method_threshold(path, args.process)
     elif args.method == 2:
-        method_newThreshold(path,args.process)
+        method_newThreshold(path, args.process)
     elif args.method == 3:
-        predict(path, ['data/output/imgs/'+name[10:] for name in path], args.load, args.scale, args.mask_threshold)
+        predict(path, args.load, args.scale, args.mask_threshold)
+        for exName in filter(lambda x: x != '.DS_Store', os.listdir('data/output')):
+            draw_bar(exName, os.listdir('data/output/' + exName + '/csv'))

predict.py

@@ -3,10 +3,13 @@ import numpy as np
 import torch
 import torch.nn.functional as F
 from PIL import Image
+import cv2 as cv
+from tqdm import tqdm
 from torchvision import transforms
 
 from unet import UNet
 from utils.dataset import BasicDataset
+from cvBasedMethod.util import save_img,calcRes
 
 
 def predict_img(net, full_img, device, scale_factor = 1, out_threshold = 0.5):
@@ -30,14 +33,7 @@ def predict_img(net, full_img, device, scale_factor = 1, out_threshold = 0.5):
     return full_mask > out_threshold
 
 
-def mask_to_image(mask):
-    return Image.fromarray((mask * 255).astype(np.uint8))
-
-
-def predict(img_name, outdir, model, scale, mask_threshold):
-    in_files = img_name
-    out_files = outdir
-
+def predict(file_names, model, scale, mask_threshold):
     net = UNet(n_channels = 1, n_classes = 1)
 
     logging.info("Loading model {}".format(model))
@@ -49,15 +45,12 @@ def predict(img_name, outdir, model, scale, mask_threshold):
 
     logging.info("Model loaded !")
 
-    for i, fn in enumerate(in_files):
-        logging.info("\nPredicting image {} ...".format(fn))
-
-        img = Image.open(fn)
-
+    for i, fn in enumerate(tqdm(file_names)):
+        logging.info("\nPredicting image {} ...".format(fn[0]+'/'+fn[1]))
+        img = Image.open('data/imgs/' + fn[0] + '/' + fn[1])
         mask = predict_img(net = net, full_img = img, scale_factor = scale, out_threshold = mask_threshold,
                            device = device)
-        #out_fn = out_files[i]
-        result = mask_to_image(mask)
-        result.save(out_files[i])
 
-        logging.info("Mask saved to {}".format(out_files[i]))
+        result = (mask * 255).astype(np.uint8)  # result.save(out_files[i])  # logging.info("Mask saved to {}".format(out_files[i]))
\ No newline at end of file
+        save_img({'ori':img,'mask':result},fn[0],fn[1])
+        calcRes(cv.cvtColor(np.asarray(img), cv.COLOR_RGB2BGR),result,fn[0],fn[1][:-4])
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