def test_get_img_info_uint16_tif_s3(self):
self.set_s3_args()
ingest_job = IngestJob(self.args)
z_slice = 0
# create an image
img_fname = ingest_job.get_img_fname(z_slice)
create_img_file(ingest_job.img_size[0], ingest_job.img_size[1],
self.args.datatype, self.args.extension, img_fname)
# put the image on a bucket
s3 = boto3.resource('s3')
with open(img_fname, 'rb') as img_file:
s3.Bucket(self.args.s3_bucket_name).put_object(Key=img_fname,
Body=img_file)
# get info on that image
im_width, im_height, im_datatype = ingest_job.get_img_info(z_slice)
# assert the info is correct
im = np.array(Image.open(img_fname))
assert im_width == im.shape[1]
assert im_height == im.shape[0]
assert im_datatype == im.dtype
s3.Bucket(self.args.s3_bucket_name).delete_objects(
Delete={'Objects': [{
'Key': img_fname
}]})
os.remove(ingest_job.get_log_fname())
os.remove(img_fname)
def test_get_img_fname_channel(self):
self.args.base_filename = 'img_<ch>_<p:4>'
self.args.base_path = 'local_img_<ch>_test_data/'
ingest_job = IngestJob(self.args)
img_fname = ingest_job.get_img_fname(0)
assert img_fname == 'local_img_{0}_test_data/img_{0}_{1:04d}.tif'.format(
self.args.channel, 0)
os.remove(ingest_job.get_log_fname())
def test_get_img_fname(self):
self.args.extension = 'tif'
ingest_job = IngestJob(self.args)
img_fname = ingest_job.get_img_fname(0)
img_fname_test = '{}img_{:04d}.{}'.format(self.args.base_path, 0,
self.args.extension)
assert img_fname == img_fname_test
os.remove(ingest_job.get_log_fname())
def test_load_img_local(self):
ingest_job = IngestJob(self.args)
z_slice = 0
img_fname = ingest_job.get_img_fname(z_slice)
create_img_file(ingest_job.img_size[0], ingest_job.img_size[1],
self.args.datatype, self.args.extension, img_fname)
im = ingest_job.load_img(z_slice)
img_local_test = np.array(Image.open(img_fname))
assert np.array_equal(im, img_local_test)
os.remove(ingest_job.get_log_fname())
os.remove(img_fname)
def test_get_img_info_uint16_png(self):
file_format = 'png'
self.args.file_format = file_format
ingest_job = IngestJob(self.args)
z_slice = 0
img_fname = ingest_job.get_img_fname(z_slice)
create_img_file(ingest_job.img_size[0], ingest_job.img_size[1],
self.args.datatype, self.args.extension, img_fname)
im_width, im_height, im_datatype = ingest_job.get_img_info(z_slice)
assert im_width == ingest_job.img_size[0]
assert im_height == ingest_job.img_size[1]
assert im_datatype == self.args.datatype
os.remove(ingest_job.get_log_fname())
os.remove(img_fname)
def test_create_local_IngestJob_neg_z_extents_offset_range(self):
self.args.z_extent = [-1000, 2000]
self.args.z_range = [-10, 10]
self.args.offset_extents = True
ingest_job = IngestJob(self.args)
assert ingest_job.x_extent == [0, 1000]
assert ingest_job.offsets == [0, 0, 1000]
assert ingest_job.z_extent == [0, 3000]
assert ingest_job.z_range == [-10, 10]
img_fname = ingest_job.get_img_fname(-5)
# assert that first tif image has a file name with the negative original extent of the data
img_fname_test = '{}img_{:04d}.{}'.format(self.args.base_path, -5,
self.args.extension)
assert img_fname == img_fname_test
os.remove(ingest_job.get_log_fname())
def test_get_img_info_uint64_tif(self):
file_format = 'tif'
dtype = 'uint64'
self.args.file_format = file_format
self.args.datatype = dtype
self.args.source_channel = 'def_files'
ingest_job = IngestJob(self.args)
z_slice = 0
img_fname = ingest_job.get_img_fname(z_slice)
create_img_file(ingest_job.img_size[0], ingest_job.img_size[1],
self.args.datatype, self.args.extension, img_fname)
im_width, im_height, im_datatype = ingest_job.get_img_info(z_slice)
assert im_width == ingest_job.img_size[0]
assert im_height == ingest_job.img_size[1]
assert im_datatype == self.args.datatype
os.remove(ingest_job.get_log_fname())
os.remove(img_fname)
