Skip to content
This repository has been archived by the owner on Jul 2, 2020. It is now read-only.

Commit

Permalink
reformat matchingarea.py
Browse files Browse the repository at this point in the history
  • Loading branch information
@DaisukeMiyamoto
DaisukeMiyamoto committed Feb 13, 2017
1 parent 2e4d0f5 commit f117c55
Showing 1 changed file with 24 additions and 36 deletions.
60 changes: 24 additions & 36 deletions registration/MatchingArea.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,9 +15,8 @@ class MatchingArea:
SECTION_AREA_BIAS = 10.0
PROCESSED_THRESHOLD = 50
N_LABELED_AREA = 40


def __init__(self, homedir=None, labeled_filename=None):

def __init__(self, homedir=None, labeled_filename=None):

if homedir is None:
homedir = os.path.join('/', 'data', 'registration', 'Test')
Expand All @@ -28,15 +27,14 @@ def __init__(self, homedir=None, labeled_filename=None):
if labeled_filename is None:
self.labeled_filename = os.path.join(homedir, 'reslice_labeled_8bit', 'reslice_labeled%04d.tif')


self.ish_dir = os.path.join(homedir, 'work4')
self.ish_color_dir = os.path.join(homedir, 'work5')
self.metric_dir = os.path.join(homedir, 'metric')

self.result_dir = os.path.join(homedir, 'area')
if not os.path.exists(self.result_dir):
os.mkdir(self.result_dir)

self.result_log = []

def matching(self, filename):
Expand All @@ -46,18 +44,17 @@ def matching(self, filename):
image_ish_color = self._read_ish_color_file(filename_base)

image_labeled = Image.open(self.labeled_filename % slice_id)
#print(self.labeled_filename % slice_id)
# print(self.labeled_filename % slice_id)

#labeled_intensity = self._matching_method_threashold(image_ish, image_labeled)
# labeled_intensity = self._matching_method_threashold(image_ish, image_labeled)
labeled_intensity = self._matching_method_threashold_color(filename_base, image_ish_color, image_labeled)

self._write_result_file(filename_base, labeled_intensity)

line = '%s' % filename_base
for k, v in labeled_intensity.items():
line += ', %f' % v
self.result_log.append(line+'\n')

self.result_log.append(line + '\n')

def _matching_method_threashold(self, image_ish, image_labeled):
# Initialize data
Expand All @@ -73,24 +70,20 @@ def _matching_method_threashold(self, image_ish, image_labeled):
labeled_intensity[i] = 0
labeled_intensity_per_area[i] = 0.0


# Process
for val_ish, val_labeled in zip(data_ish, data_labeled):
labeled_area[val_labeled] += 1
if val_labeled != 0 and val_ish < self.INTENSITY_THRESHOLD:
labeled_intensity[val_labeled] += 1


# Normalize intensity by volume
for i in range(self.N_LABELED_AREA):
if labeled_area[i] > self.SECTION_AREA_THRESHOLD:
labeled_intensity_per_area[i] = float(labeled_intensity[i]) / (labeled_area[i] + self.SECTION_AREA_BIAS)


#return labeled_intensity
# return labeled_intensity
return labeled_intensity_per_area



def _matching_method_threashold_color(self, filename_base, image_ish, image_labeled):
# Initialize data
data_ish = image_ish.getdata()
Expand All @@ -105,55 +98,51 @@ def _matching_method_threashold_color(self, filename_base, image_ish, image_labe
labeled_intensity[i] = 0
labeled_intensity_per_area[i] = 0.0


# Process
processed_data = []
for val_ish, val_labeled in zip(data_ish, data_labeled):
labeled_area[val_labeled] += 1
ave = (val_ish[0] + val_ish[1] + val_ish[2])/3
value = val_ish[2]*2 - (val_ish[0] + val_ish[1])
ave = (val_ish[0] + val_ish[1] + val_ish[2]) / 3
value = val_ish[2] * 2 - (val_ish[0] + val_ish[1])
processed_data.append(value)
if val_labeled != 0 and ave > self.INTENSITY_THRESHOLD:
if val_labeled != 0 and ave > self.INTENSITY_THRESHOLD:
if value > self.PROCESSED_THRESHOLD:
labeled_intensity[val_labeled] += 1

self.save_processed_image(os.path.join('..', 'private', 'processed_image', filename_base+'.tif'), processed_data)

self.save_processed_image(os.path.join('..', 'private', 'processed_image', filename_base + '.tif'),
processed_data)

# Normalize intensity by volume
for i in range(self.N_LABELED_AREA):
if labeled_area[i] > self.SECTION_AREA_THRESHOLD:
labeled_intensity_per_area[i] = float(labeled_intensity[i]) / (labeled_area[i] + self.SECTION_AREA_BIAS)


#return labeled_intensity
# return labeled_intensity
return labeled_intensity_per_area


def _read_ish_file(self, filename_base):

metric = {}
metric_filename = os.path.join(self.metric_dir, filename_base+'.txt')
metric_filename = os.path.join(self.metric_dir, filename_base + '.txt')

with open(metric_filename, 'r') as f:
reader = csv.reader(f)
for row in reader:
metric[int(row[0])] = float(row[1])
min_slice_id = min(metric.items(), key=lambda x:x[1])[0]
#print min_slice

min_slice_id = min(metric.items(), key=lambda x: x[1])[0]
# print min_slice
regist_filename = os.path.join(self.ish_dir, filename_base, ('%04d.tif' % min_slice_id))
#print regist_filename
# print regist_filename

return Image.open(regist_filename), min_slice_id


def _read_ish_color_file(self, filename_base):
ish_color_filename = os.path.join(self.ish_color_dir, filename_base+'.tif')
ish_color_filename = os.path.join(self.ish_color_dir, filename_base + '.tif')
return Image.open(ish_color_filename)


def _write_result_file(self, filename_base, labeled_intensity):
result_filename = os.path.join(self.result_dir, filename_base+'.txt')
result_filename = os.path.join(self.result_dir, filename_base + '.txt')
print result_filename
with open(result_filename, 'w') as f:
for k, v in labeled_intensity.items():
Expand All @@ -162,7 +151,7 @@ def _write_result_file(self, filename_base, labeled_intensity):
def write_log(self, filename):
with open(filename, 'w') as f:
f.writelines(self.result_log)

def save_processed_image(self, filename, data):
processed = Image.new('L', (512, 256), 0)
processed.putdata(data)
Expand All @@ -172,7 +161,7 @@ def save_processed_image(self, filename, data):

if __name__ == '__main__':

#filelistname = os.path.join('/', 'data', 'registration', 'Test', 'filelist_all0.txt')
# filelistname = os.path.join('/', 'data', 'registration', 'Test', 'filelist_all0.txt')
filelistname = os.path.join('..', 'private', 'filelist_all0.txt')
filelist = RegistrationCommon.read_filelist(filelistname)

Expand All @@ -182,4 +171,3 @@ def save_processed_image(self, filename, data):
matchingarea.matching(filename)

matchingarea.write_log(os.path.join('..', 'private', 'intensity_all.txt'))

0 comments on commit f117c55

Please sign in to comment.