def test_bad_id():
reader = ome_files.OMETIFFReader()
filename = str(uuid.uuid4())
with pytest.raises(RuntimeError):
reader.set_id(filename)
with pytest.raises(TypeError):
reader.set_id(0)
def get_metadata(filename):
"""
Simple wrapper for retrieving the 5D dimensions of an image from omefiles
"""
import ome_files
reader = ome_files.OMETIFFReader()
reader.set_id(filename)
H, W, Z, T, C = reader.get_size_y(), reader.get_size_x(
), reader.get_size_z(), reader.get_size_t(), reader.get_size_c()
reader.close()
return H, W, Z, T, C
def read_plane(filename, plane):
"""
Simple wrapper for ome_files reader, choosing the correct ZCT coords from the plane value
"""
import ome_files
reader = ome_files.OMETIFFReader()
reader.set_id(filename)
pixels = reader.open_array(plane)
Z, C, T = reader.get_zct_coords(plane)
reader.close()
return pixels, Z, C, T
def dump(ome_tiff_fn):
reader = ome_files.OMETIFFReader()
reader.set_id(ome_tiff_fn)
img_count = reader.get_image_count()
H, W = reader.get_size_y(), reader.get_size_x()
dtype = np.dtype(reader.get_pixel_dtype())
rgb = reader.get_rgb_channel_count(0)
interleaved = reader.is_interleaved(0)
print("image count: %d" % img_count)
print("RGB sub-channels: %d (%sinterleaved)" %
(rgb, "" if interleaved else "non-"))
print("image size: %d x %d" % (W, H))
print("pixel type:", dtype)
for i in range(img_count):
pixels = reader.open_bytes_simple(i)
out_fn = "plane_%d.tiff" % i
print("writing %s" % out_fn)
with closing(TIFF.open(out_fn, mode="w")) as fo:
fo.write_image(pixels, write_rgb=(rgb > 1))
reader.close()
def setup_method(self):
self.reader = ome_files.OMETIFFReader()
# -*- coding: utf-8 -*-
"""
Created on Tue Jun 5 17:21:10 2018
@author: Erick Martins Ratamero
"""
import sys
reload(sys)
sys.setdefaultencoding('utf8')
#%matplotlib inline
import numpy as np
import matplotlib.pyplot as plt
import ome_files
reader = ome_files.OMETIFFReader()
reader.set_id(
'/home/erick/Nextcloud/CMCB/Michael_protrusions/smallstack.ome.tiff')
# calculate number of planes
no_planes = reader.get_image_count()
print(no_planes)
z = reader.get_size_z()
print(z)
# for each plane:
for plane in range(no_planes):
pixels = reader.open_bytes_simple(plane)
# for each non-zero pixel:
# get neighbourhood (adjust for borders)
# fit circle to neighbourhood