def main():
"""
utils.create_png_images:
Creates PNGs for all the subjects in the subject list. The NIFTI images from where these PNGs are generated
must have been downloaded first (step 1).
Make sure that you set NUM_LABELS, HISTOLOGY_RANGE_MIN and HISTOLOGY_RANGE_MAX in the configuration file before
creating running this step.
The HISTOLOGY_RANGE_MIN and HISTOLOGY_RANGE_MAX parameters determine how histology values are mapped to labels.
These two parameters correspond to cmin, and cmax in scipy.misc.bytescale
See: https://docs.scipy.org/doc/scipy-0.18.1/reference/generated/scipy.misc.bytescale.html
"""
config = dh_read_config(
'/home/dcantor/projects/deephisto/code/config_neuronal_density.ini')
#config = dh_read_config('/home/dcantor/projects/deephisto/code/config_field_fraction.ini')
subjects = dh_load_subjects(config)
utils = ImageUtils(config)
dh_get_histo_range(config)
# comment this for loop if you only want to run dh_get_histo_range. This will report the domain values (histology)
for s in subjects:
print s
utils.create_png_images(s)
def main():
# config = dh_read_config('/home/dcantor/projects/deephisto/code/config_neuronal_density.ini')
config = dh_read_config(
'/home/dcantor/projects/deephisto/code/config_field_fraction.ini')
subjects = dh_load_subjects(config)
for s in subjects:
dh_visual_inspection(config, s, 0, 0)
def main():
"""
This is the first step you need to run on your DeepHisto project.
Use one of the configuration files or create your own.
>> config_neuronal_densitiy.ini
>> config_field_fraction.ini
"""
config = dh_read_config('/home/dcantor/projects/deephisto/code/config_neuronal_density.ini')
#config = dh_read_config('/home/dcantor/projects/deephisto/code/config_field_fraction.ini')
subjects = dh_load_subjects(config)
dog = ImageRetriever(config)
for s in subjects:
dog.retrieve(s)
def main():
config = dh_read_config('/home/dcantor/projects/deephisto/code/config_neuronal_density.ini')
#config = dh_read_config('/home/dcantor/projects/deephisto/code/config_field_fraction.ini')
dh_create_dataset(config)
def main():
#config = dh_read_config('/home/dcantor/projects/deephisto/code/config_neuronal_density.ini')
#config = dh_read_config('/home/dcantor/projects/deephisto/code/config_field_fraction.ini')
config = dh_read_config('/home/dcantor/projects/deephisto/code/config_neuronal_density_rt.ini')
net = NetBuilder_fcn8(config)
net.make()
def main():
config = dh_read_config(
'/home/dcantor/projects/deephisto/code/config_neuronal_density.ini')
#config = dh_read_config('/home/dcantor/projects/deephisto/code/config_field_fraction.ini')
dh_unpack_annotations(config)
import os
from deephisto import Locations
from config import dh_load_subjects, dh_read_config
#config = dh_read_config('/home/dcantor/projects/deephisto/code/config_neuronal_density.ini')
config = dh_read_config(
'/home/dcantor/projects/deephisto/code/config_field_fraction.ini')
locations = Locations(config)
subjects = dh_load_subjects(config)
for subject in subjects:
locations.set_subject(subject)
files = os.listdir(locations.MASK_DIR)
print
print locations.MASK_DIR
for f in files:
if f.startswith('A_'):
A, B, C, I = f.split('_')
I1, _ = I.split('.')
change = 'A_H_%s.png' % I1
source = locations.MASK_DIR + '/' + f
target = locations.MASK_DIR + '/' + change
print source, target
os.rename(source, target)