diff --git a/docs/source/specifications/metadata.org b/docs/source/specifications/metadata.org index c7dc02b06c1e879b66dabfdfc8d8653575fbcc0f..52d514a3465236a9079a8bba3ee721b013808a28 100644 --- a/docs/source/specifications/metadata.org +++ b/docs/source/specifications/metadata.org @@ -4,7 +4,7 @@ Draft for recommended metadata for images to provide a standard interface for al * Essential data - DimensionOrder: str - Order of dimensions (e.g., TCZYX for Channel, Time, Z,Y,X) + Order of dimensions (e.g., TCZYX for Time, Channel, Z, Y, X) - PixelSize: float Size of pixel, useful for segmentation. - Channels: List[str] diff --git a/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003.tif b/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003.tif index f813c15a9c8aef8a6e629ff17e460aef4acdb630..569f33a72ab18f65c79e28e38869a4f17cd30cca 100755 Binary files a/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003.tif and b/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003.tif differ diff --git a/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003_square.tif b/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003_square.tif new file mode 100755 index 0000000000000000000000000000000000000000..f813c15a9c8aef8a6e629ff17e460aef4acdb630 Binary files /dev/null and b/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003_square.tif differ diff --git a/src/aliby/io/image.py b/src/aliby/io/image.py index 57283dc493fc226f013fb96c6e7c7d03abd05147..7e021fcdfa6e582443161addcb5d5eb9e4d8bc1d 100644 --- a/src/aliby/io/image.py +++ b/src/aliby/io/image.py @@ -5,7 +5,7 @@ Image: Loads images and registers them. Image instances loads images from a specified directory into an object that also contains image properties such as name and metadata. Pixels from images are stored in dask arrays; the standard way is to store them in 5-dimensional -arrays: T(ime point), C(channel), Z(-stack), X, Y. +arrays: T(ime point), C(channel), Z(-stack), Y, X. This module consists of a base Image class (BaseLocalImage). ImageLocalOME handles local OMERO images. ImageDir handles cases in which images are split @@ -81,8 +81,8 @@ class BaseLocalImage(ABC): 1, 1, 1, - self._meta["size_x"], self._meta["size_y"], + self._meta["size_x"], ), ) return self._rechunked_img @@ -212,9 +212,11 @@ class ImageDummy(BaseLocalImage): ) # 5 z-stacks return img + @property def name(self): pass + @property def dimorder(self): pass diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py index 26e9b9dc92e24b9cdf731363ca5432ca702e52b2..f7f47cfb316bde17a6aad3a1abc6568f9397c294 100644 --- a/src/aliby/pipeline.py +++ b/src/aliby/pipeline.py @@ -112,7 +112,7 @@ class PipelineParameters(ParametersABC): ntps_to_eval=5, ), logfile_level="INFO", - logstream_level="WARNING", + use_explog=True, ) } @@ -691,7 +691,9 @@ class Pipeline(ProcessABC): except Exception: pass - meta.run() + if config["general"]["use_explog"]: + meta.run() + meta.add_fields( # Add non-logfile metadata { "aliby_version": version("aliby"), diff --git a/src/aliby/tile/tiler.py b/src/aliby/tile/tiler.py index a3216e9eb7f0987238161a977249b4c74a1bb4dc..34aa89d1c2af76976f134a0fd38d58919cedc9bb 100644 --- a/src/aliby/tile/tiler.py +++ b/src/aliby/tile/tiler.py @@ -261,14 +261,13 @@ class Tiler(StepABC): """ imgdmy_obj = ImageDummy(parameters) dummy_image = imgdmy_obj.get_data_lazy() - dummy_omero_metadata = ( # Default to "tczyx" if image.dimorder is None - { - f"size_{dim}": dim_size - for dim, dim_size in zip( - imgdmy_obj.dimorder or "tczyx", dummy_image.shape - ) - }, - ) + # Default to "tczyx" if image.dimorder is None + dummy_omero_metadata = { + f"size_{dim}": dim_size + for dim, dim_size in zip( + imgdmy_obj.dimorder or "tczyx", dummy_image.shape + ) + } dummy_omero_metadata.update( { "channels": [