{% endfor -%}
{% for inp,val in cookiecutter._inputs|dictsort -%}
{% for out,n in cookiecutter._outputs|dictsort -%}
{% if val.type=="collection" and cookiecutter.use_bfio -%}
# Loop through files in {{ inp }} image collection and process
for i,f in enumerate({{ inp }}_files):
# Load an image
br = BioReader(Path({{ inp }}).joinpath(f))
image = np.squeeze(br.read_image())
# initialize the output
out_image = np.zeros(image.shape,dtype=br._pix['type'])
""" Do some math and science - you should replace this """
logger.info('Processing image ({}/{}): {}'.format(i,len({{ inp }}_files),f))
out_image = awesome_math_and_science_function(image)
# Write the output
bw = BioWriter(Path({{ out }}).joinpath(f),metadata=br.read_metadata())
bw.write_image(np.reshape(out_image,(br.num_y(),br.num_x(),br.num_z(),1,1)))
{%- endif %}{% endfor %}{% endfor %}
finally:
{%- if cookiecutter.use_bfio %}
# Close the javabridge regardless of successful completion
logger.info('Closing the javabridge')
jutil.kill_vm()
{%- endif %}
# Exit the program
sys.exit()
# Modify the metadata to make sure channels are written correctly
bw.num_c(len(paths))
bw._metadata.image().Pixels.channel_count = bw.num_c()
# Process the data in tiles
threads = []
count = 0
total = bw.num_c() * bw.num_z() * \
(bw.num_x()//chunk_size + 1) * (bw.num_y()//chunk_size + 1)
with ThreadPoolExecutor(cpu_count()) as executor:
for c, file in enumerate(paths):
br = BioReader(file['file'])
C = [c]
first_image = True
for z in range(br.num_z()):
Z = [z, z + 1]
for x in range(0, br.num_x(), chunk_size):
X = [x, min([x + chunk_size, br.num_x()])]
for y in range(0, br.num_y(), chunk_size):
Y = [y, min([y + chunk_size, br.num_y()])]
threads.append(
executor.submit(write_tile, br, bw, X, Y,
Z, C))
# Bioformats requires the first tile to be written
# before any other tile is written
if first_image or len(threads) == cpu_count():
threads[0].result()
del threads[0]
first_image = False
