def make_web_thumbnails(animal):
"""
This was originally getting the thumbnails from the preps/thumbnail dir but they aren't usuable.
The ones in the preps/CH1/thumbnail_aligned are much better
But we need to test if there ane aligned files, if not use the cleaned ones.
Thumbnails are always created from CH1
Args:
animal: the prep id of the animal
njobs: number of jobs for parallel computing
Returns:
nothing
"""
fileLocationManager = FileLocationManager(animal)
sqlController = SqlController(animal)
INPUT = '/home/eodonnell/DK39/cshl/jpg'
OUTPUT = os.path.join(fileLocationManager.root, animal, 'cshl/jpg')
tifs = sqlController.get_sections(animal, 1)
for i, tif in enumerate(tqdm(tifs)):
input_path = os.path.join(INPUT,
os.path.splitext(tif.file_name)[0] + '.jpg')
output_path = os.path.join(OUTPUT, str(i).zfill(3) + '.jpg')
if not os.path.exists(input_path):
continue
if os.path.exists(output_path):
continue
os.makedirs(os.path.dirname(output_path), exist_ok=True)
cmd = "convert {} {}".format(input_path, output_path)
subprocess.run(cmd, shell=True)
def make_pages(animal, fetch, layer):
templateLoader = jinja2.FileSystemLoader(searchpath="./templates")
templateEnv = jinja2.Environment(loader=templateLoader)
if 'sql' in fetch:
sqlController = SqlController(animal)
valid_sections = sqlController.get_sections(animal, 1)
container = "container.html"
else:
fileLocationManager = FileLocationManager(animal)
valid_sections = sorted(os.listdir(fileLocationManager.thumbnail_web))
container = "list_dir.html"
if layer is not None:
fileLocationManager = FileLocationManager(animal)
INPUT = os.path.join(fileLocationManager.thumbnail_web, 'points',
layer)
valid_sections = sorted(os.listdir(INPUT))
container = "list_points.html"
template = templateEnv.get_template(container)
lfiles = len(valid_sections)
outputText = template.render(animal=animal,
valid_sections=valid_sections,
lfiles=lfiles,
layer=layer)
else:
template = templateEnv.get_template(container)
lfiles = len(valid_sections)
outputText = template.render(
animal=animal, valid_sections=valid_sections, lfiles=lfiles
) # this is where to put args to the template renderer
# to save the results
filename = '{}.thumbnails.html'.format(animal)
with open(filename, "w") as fh:
fh.write(outputText)
def make_web_thumbnails(animal):
"""
This was originally getting the thumbnails from the preps/thumbnail dir but they aren't usuable.
The ones in the preps/CH1/thumbnail_aligned are much better
But we need to test if there ane aligned files, if not use the cleaned ones.
Thumbnails are always created from CH1
Args:
animal: the prep id of the animal
njobs: number of jobs for parallel computing
Returns:
nothing
"""
channel_dir = 'CH1'
fileLocationManager = FileLocationManager(animal)
sqlController = SqlController(animal)
INPUT = os.path.join(fileLocationManager.prep, channel_dir,
'thumbnail_aligned')
len_files = len(os.listdir(INPUT))
if len_files < 10:
INPUT = os.path.join(fileLocationManager.prep, channel_dir,
'thumbnail_cleaned')
##### Check if files in dir are valid
error = test_dir(animal, INPUT, downsample=True, same_size=True)
if len(error) > 0:
print(error)
sys.exit()
OUTPUT = fileLocationManager.thumbnail_web
os.makedirs(OUTPUT, exist_ok=True)
tifs = sqlController.get_sections(animal, 1)
for i, tif in enumerate(tqdm(tifs)):
input_path = os.path.join(INPUT, str(i).zfill(3) + '.tif')
output_path = os.path.join(OUTPUT,
os.path.splitext(tif.file_name)[0] + '.png')
if not os.path.exists(input_path):
continue
if os.path.exists(output_path):
continue
original = Image.open(input_path)
original.save(output_path, format="png")
def fix_tifs(animal, channel):
sqlController = SqlController(animal)
fileLocationManager = FileLocationManager(animal)
dir = fileLocationManager.tif
db_files = sqlController.get_sections(animal, channel)
source_files = []
source_keys = []
for tif in db_files:
source_files.append(tif.file_name)
source_keys.append(tif.id)
files = os.listdir(dir)
files = [file for file in files if 'C{}.tif'.format(channel) in file]
missing_files = list(set(source_files) - set(files))
for i, missing in enumerate(missing_files):
#pass
file_id = source_keys[source_files.index(missing)]
section = sqlController.get_section(file_id)
print(i, missing, file_id, section.id, section.file_name)
make_tif(animal, section.tif_id, file_id, testing=False)
def make_full_resolution(animal, channel):
"""
Args:
animal: the prep id of the animal
channel: the channel of the stack to process
compress: Use the default LZW compression, otherwise just copy the file with the correct name
Returns:
list of commands
"""
fileLocationManager = FileLocationManager(animal)
sqlController = SqlController(animal)
if 'thion' in sqlController.histology.counterstain:
sqlController.set_task(animal, CREATE_CHANNEL_2_FULL_RES)
sqlController.set_task(animal, CREATE_CHANNEL_3_FULL_RES)
INPUT = os.path.join(fileLocationManager.tif)
##### Check if files in dir are valid
OUTPUT = os.path.join(fileLocationManager.prep, f'CH{channel}', 'full')
os.makedirs(OUTPUT, exist_ok=True)
sections = sqlController.get_sections(animal, channel)
for section_number, section in enumerate(tqdm(sections)):
input_path = os.path.join(INPUT, section.file_name)
output_path = os.path.join(OUTPUT,
str(section_number).zfill(3) + '.tif')
if not os.path.exists(input_path):
#print('Input tif does not exist', input_path)
continue
if os.path.exists(output_path):
continue
copyfile(input_path, output_path)
width, height = get_image_size(input_path)
sqlController.update_tif(section.id, width, height)
def make_histogram(animal, channel):
"""
This method creates an individual histogram for each tif file by channel.
Args:
animal: the prep id of the animal
channel: the channel of the stack to process {1,2,3}
Returns:
nothing
"""
logger = get_logger(animal)
fileLocationManager = FileLocationManager(animal)
sqlController = SqlController(animal)
INPUT = os.path.join(fileLocationManager.prep, f'CH{channel}', 'thumbnail')
MASK_INPUT = fileLocationManager.thumbnail_masked
tifs = sqlController.get_sections(animal, channel)
error = test_dir(animal, INPUT, downsample=True, same_size=False)
if len(tifs) == 0:
error += " No sections in the database"
if len(error) > 0:
print(error)
sys.exit()
ch_dir = f'CH{channel}'
OUTPUT = os.path.join(fileLocationManager.histogram, ch_dir)
os.makedirs(OUTPUT, exist_ok=True)
progress_id = sqlController.get_progress_id(True, channel, 'HISTOGRAM')
sqlController.set_task(animal, progress_id)
for i, tif in enumerate(tqdm(tifs)):
filename = str(i).zfill(3) + '.tif'
input_path = os.path.join(INPUT, filename)
mask_path = os.path.join(MASK_INPUT, filename)
output_path = os.path.join(OUTPUT,
os.path.splitext(tif.file_name)[0] + '.png')
if not os.path.exists(input_path):
print('Input tif does not exist', input_path)
continue
if os.path.exists(output_path):
continue
try:
img = io.imread(input_path)
except:
logger.warning(f'Could not open {input_path}')
continue
try:
mask = io.imread(mask_path)
except:
logger.warning(f'Could not open {mask_path}')
continue
img = cv2.bitwise_and(img, img, mask=mask)
if img.shape[0] * img.shape[1] > 1000000000:
scale = 1 / float(2)
img = img[::int(1. / scale), ::int(1. / scale)]
try:
flat = img.flatten()
except:
logger.warning(f'Could not flat {input_path}')
continue
fig = plt.figure()
plt.rcParams['figure.figsize'] = [10, 6]
plt.hist(flat, flat.max(), [0, 10000], color=COLORS[channel])
plt.style.use('ggplot')
plt.yscale('log')
plt.grid(axis='y', alpha=0.75)
plt.xlabel('Value')
plt.ylabel('Frequency')
plt.title(f'{tif.file_name} @16bit')
plt.close()
fig.savefig(output_path, bbox_inches='tight')
