refactor project name

src/lif_converters/__init__.py → src/fractal_lif_converters/__init__.py

@@ -2,7 +2,7 @@
 
 from importlib.metadata import PackageNotFoundError, version
 
-from lif_converters.wrappers import (
+from fractal_lif_converters.wrappers import (
     convert_lif_plate_to_omezarr,
     convert_lif_scene_to_omezarr,
 )

src/lif_converters/convert_lif_compute_task.py → src/fractal_lif_converters/convert_lif_compute_task.py

@@ -4,7 +4,7 @@
 
 from pydantic import BaseModel, Field, validate_call
 
-from lif_converters.utils.converter_utils import (
+from fractal_lif_converters.utils.converter_utils import (
     export_ngff_plate_acquisition,
     export_ngff_single_scene,
 )

src/lif_converters/convert_lif_plate_init_task.py → src/fractal_lif_converters/convert_lif_plate_init_task.py

@@ -7,8 +7,8 @@
 from fractal_tasks_core.utils import logger
 from pydantic import Field, validate_call
 
-from lif_converters.convert_lif_compute_task import ComputeInputModel
-from lif_converters.utils import (
+from fractal_lif_converters.convert_lif_compute_task import ComputeInputModel
+from fractal_lif_converters.utils import (
     LifFormatNotSupported,
     TimeSeriesNotSupported,
     setup_plate_ome_zarr,

src/lif_converters/convert_lif_scene_init_task.py → src/fractal_lif_converters/convert_lif_scene_init_task.py

@@ -8,7 +8,7 @@
 from fractal_tasks_core.utils import logger
 from pydantic import Field, validate_call
 
-from lif_converters.convert_lif_compute_task import ComputeInputModel
+from fractal_lif_converters.convert_lif_compute_task import ComputeInputModel
 
 
 def _rename_scene(scene_name: str):

src/lif_converters/utils/__init__.py → src/fractal_lif_converters/utils/__init__.py

@@ -1,7 +1,10 @@
 """Utils to convert lif files"""
 
-from lif_converters.utils._errors import LifFormatNotSupported, TimeSeriesNotSupported
-from lif_converters.utils.converter_utils import (
+from fractal_lif_converters.utils._errors import (
+    LifFormatNotSupported,
+    TimeSeriesNotSupported,
+)
+from fractal_lif_converters.utils.converter_utils import (
     _export_acquisition_to_zarr,
     setup_plate_ome_zarr,
 )

src/lif_converters/utils/converter_utils.py → src/fractal_lif_converters/utils/converter_utils.py

@@ -14,9 +14,9 @@
 from fractal_tasks_core.utils import logger
 from pandas import DataFrame
 
-from lif_converters.utils.lif_utils import build_grid_mapping
-from lif_converters.utils.ngff_image_meta_utils import generate_ngff_metadata
-from lif_converters.utils.ngff_plate_meta_utils import (
+from fractal_lif_converters.utils.lif_utils import build_grid_mapping
+from fractal_lif_converters.utils.ngff_image_meta_utils import generate_ngff_metadata
+from fractal_lif_converters.utils.ngff_plate_meta_utils import (
     PlateScene,
     build_acquisition_path,
     build_well_path,
@@ -150,8 +150,8 @@ def _export_acquisition_to_zarr(
         dim.t,
         num_channels,
         dim.z,
-        grid_size_y * size_y,
-        grid_size_x * size_x,
+        grid_size_x * size_y,
+        grid_size_y * size_x,
     ]
     chunk_shape = [1, 1, 1, dim.y, dim.x]
 
@@ -193,6 +193,18 @@ def _export_acquisition_to_zarr(
                     slice(j * size_x, (j + 1) * size_x),
                 )
 
+            """
+            print(slices)
+            print(
+                _c,
+                _z,
+                i * size_y,
+                (i + 1) * size_y,
+                j * size_x,
+                (j + 1) * size_x,
+            )
+            print(high_res_array.shape)
+            """
             high_res_array[slices] = frame
 
     # Build the pyramid for the high resolution data

src/lif_converters/utils/lif_utils.py → src/fractal_lif_converters/utils/lif_utils.py

@@ -5,7 +5,7 @@
 import numpy as np
 from readlif.reader import LifFile, LifImage
 
-from lif_converters.utils import LifFormatNotSupported
+from fractal_lif_converters.utils import LifFormatNotSupported
 
 
 def find_shape_um(image: LifImage) -> tuple[float, float, float]:

src/lif_converters/utils/ngff_plate_meta_utils.py → src/fractal_lif_converters/utils/ngff_plate_meta_utils.py

@@ -14,7 +14,7 @@
     WellInPlate,
 )
 
-from lif_converters.utils import LifFormatNotSupported
+from fractal_lif_converters.utils import LifFormatNotSupported
 
 
 def column_formatting(column: int | str) -> str:

src/lif_converters/wrappers.py → src/fractal_lif_converters/wrappers.py

@@ -2,11 +2,13 @@
 
 from pathlib import Path
 
-from lif_converters.convert_lif_compute_task import (
+from fractal_lif_converters.convert_lif_compute_task import (
     convert_lif_compute_task,
 )
-from lif_converters.convert_lif_plate_init_task import convert_lif_plate_init_task
-from lif_converters.convert_lif_scene_init_task import (
+from fractal_lif_converters.convert_lif_plate_init_task import (
+    convert_lif_plate_init_task,
+)
+from fractal_lif_converters.convert_lif_scene_init_task import (
     convert_lif_scene_init_task,
 )
 

tests/test_lif_converter_task.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from lif_converters.wrappers import (
+from fractal_lif_converters.wrappers import (
     convert_lif_plate_to_omezarr,
     convert_lif_scene_to_omezarr,
 )