Split into smaller subclasses

.gitignore

@@ -173,4 +173,5 @@ data/CellDivision_T=10_Z=15_CH=2_DCV_small.czi
 /data/Tumor_HE_Orig_small_Label.czi
 /data/Tumor_HE_Orig_small_SlidePreview.czi
 /data/est_ngff_plate.zarr
-/data/est_ngff_plate.zarr
+/data/est_ngff_plate.zarr
+*.old

README.md

@@ -27,10 +27,10 @@ pip install czitools[all]
 Please check [use_metadata_tools.py](https://github.com/sebi06/czitools/blob/main/demo/scripts/use_metadata_tools.py) for some examples.
 
 ```python
-# get the metadata at once as one big class
+# get the metadata_tools at once as one big class
 mdata = czimd.CziMetadata(filepath)
 
-# get only specific metadata
+# get only specific metadata_tools
 czi_dimensions = czimd.CziDimensions(filepath)
 print("SizeS: ", czi_dimensions.SizeS)
 print("SizeT: ", czi_dimensions.SizeT)
@@ -45,7 +45,7 @@ xmlfile = czimd.writexml(filepath)
 # get info about the channels
 czi_channels = czimd.CziChannelInfo(filepath)
 
-# get the complete metadata from the CZI as one big object
+# get the complete metadata_tools from the CZI as one big object
 czimd_complete = czimd.get_metadata_as_object(filepath)
 
 # get an object containing only the dimension information

demo/scripts/read_attachment_images.py

@@ -2,8 +2,8 @@
 from czitools.read_tools import AttachmentType
 from pathlib import Path
 import os
-from czitools.czi_metadata import CziMetadata
-from czitools.metadata.attachment import CziAttachments
+from czitools.metadata_tools.czi_metadata import CziMetadata
+from czitools.metadata_tools.attachment import CziAttachments
 
 # adapt to your needs
 defaultdir = Path(Path(__file__).resolve().parents[2]) / "data"
@@ -14,7 +14,7 @@
 # filepath = r"Tumor_HE_Orig_small.czi"
 # filepath = r"CellDivision_T=10_Z=15_CH=2_DCV_small.czi"
 
-# read all metadata and check for the attachment images
+# read all metadata_tools and check for the attachment images
 md = CziMetadata(filepath)
 print(f"CZI Image has Label {md.attachments.has_label}")
 print(f"CZI Image has SlidePreview {md.attachments.has_preview}")

demo/scripts/read_czi_aicsimageio.py

@@ -11,8 +11,9 @@
 
 import napari
 from aicsimageio import AICSImage
-from czitools import napari_tools, czi_metadata as czimd
-from czitools.tools import misc
+from czitools import napari_tools
+from czitools.metadata_tools import czi_metadata as czimd
+from czitools.utils import misc
 import os
 from pathlib import Path
 
@@ -28,7 +29,7 @@
 )
 print(filepath)
 
-# get the complete metadata using czitools
+# get the complete metadata_tools using czitools
 mdata = czimd.CziMetadata(filepath)
 
 # test using AICSImageIO (needs to be installed)

demo/scripts/use_metadata_tools.py

@@ -9,33 +9,33 @@
 #
 #################################################################
 
-from czitools.czi_metadata import CziMetadata, writexml, get_metadata_as_object, obj2dict
-from czitools.metadata.dimension import CziDimensions
-from czitools.metadata.boundingbox import CziBoundingBox
-from czitools.metadata.channel import CziChannelInfo
-from czitools.metadata.scaling import CziScaling
-from czitools.metadata.sample import CziSampleInfo
-from czitools.metadata.objective import CziObjectives
-from czitools.metadata.microscope import CziMicroscope
-from czitools.metadata.add_metadata import CziAddMetaData
-from czitools.metadata.detector import CziDetector
-from czitools.tools import misc
+from czitools.metadata_tools.czi_metadata import CziMetadata, writexml, get_metadata_as_object, obj2dict
+from czitools.metadata_tools.dimension import CziDimensions
+from czitools.metadata_tools.boundingbox import CziBoundingBox
+from czitools.metadata_tools.channel import CziChannelInfo
+from czitools.metadata_tools.scaling import CziScaling
+from czitools.metadata_tools.sample import CziSampleInfo
+from czitools.metadata_tools.objective import CziObjectives
+from czitools.metadata_tools.microscope import CziMicroscope
+from czitools.metadata_tools.add_metadata import CziAddMetaData
+from czitools.metadata_tools.detector import CziDetector
+from czitools.utils import misc
 from pathlib import Path
 
 # adapt to your needs
 defaultdir = Path(Path(__file__).resolve().parents[2]) / "data"
 
 # open s simple dialog to select a CZI file
 filepath = misc.openfile(directory=str(defaultdir),
-                               title="Open CZI Image File",
-                               ftypename="CZI Files",
-                               extension="*.czi")
+                         title="Open CZI Image File",
+                         ftypename="CZI Files",
+                         extension="*.czi")
 print(filepath)
 
-# get the metadata at once as one big class
+# get the metadata_tools at once as one big class
 mdata = CziMetadata(filepath)
 
-# get only specific metadata
+# get only specific metadata_tools
 czi_dimensions = CziDimensions(filepath)
 print("SizeS: ", czi_dimensions.SizeS)
 print("SizeT: ", czi_dimensions.SizeT)
@@ -50,7 +50,7 @@
 # get info about the channels
 czi_channels = CziChannelInfo(filepath)
 
-# get the complete metadata from the CZI as one big object
+# get the complete metadata_tools from the CZI as one big object
 czimd_complete = get_metadata_as_object(filepath)
 
 # get an object containing only the dimension information
@@ -83,7 +83,7 @@
 print(czi_bbox.total_rect)
 print(czi_bbox.total_bounding_box["C"])
 
-# get selected metadata as a dictionary
+# get selected metadata_tools as a dictionary
 mdata_dict = obj2dict(mdata)
 
 # and convert to pd.DataFrame

demo/scripts/use_read_tools.py

@@ -11,7 +11,7 @@
 
 from czitools import read_tools
 from czitools import napari_tools
-from czitools.tools import misc
+from czitools.utils import misc
 import napari
 from pathlib import Path
 

demo/scripts/use_write_tools.py

@@ -9,7 +9,8 @@
 #
 #################################################################
 
-from czitools import read_tools, write_tools, czi_metadata as czimd
+from czitools import read_tools, write_tools
+from czitools.metadata_tools import czi_metadata as czimd
 import napari
 from pathlib import Path
 
@@ -18,7 +19,7 @@
 filepath = defaultdir / "CellDivision_T3_Z5_CH2_X240_Y170.czi"
 zarr_path = Path(str(filepath)[:-4] + ".ome.zarr")
 
-# get the metadata at once as one big class
+# get the metadata_tools at once as one big class
 mdata = czimd.CziMetadata(filepath)
 print("Number of Scenes: ", mdata.image.SizeS)
 scene_id = 0

src/czitools/_tests/test_bounding_box.py

@@ -1,4 +1,4 @@
-from czitools import czi_metadata as czimd
+from czitools.metadata_tools import czi_metadata as czimd
 from pathlib import Path
 from pylibCZIrw import czi
 import pytest

src/czitools/_tests/test_channelinfo.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from czitools import czi_metadata as czimd
+from czitools.metadata_tools import czi_metadata as czimd
 import pytest
 from typing import List
 

src/czitools/_tests/test_czimd_box.py

@@ -1,4 +1,4 @@
-from czitools import czi_metadata as czimd
+from czitools.metadata_tools import czi_metadata as czimd
 from pathlib import Path
 import pytest
 from typing import List

src/czitools/_tests/test_dimensions.py

@@ -1,4 +1,4 @@
-from czitools import czi_metadata as czimd
+from czitools.metadata_tools import czi_metadata as czimd
 from pathlib import Path
 import pytest
 from typing import List, Any

src/czitools/_tests/test_info.py

@@ -1,4 +1,4 @@
-from czitools import czi_metadata as czimd
+from czitools.metadata_tools import czi_metadata as czimd
 from pathlib import Path
 import pytest
 from typing import List

src/czitools/_tests/test_instrument.py

@@ -1,4 +1,4 @@
-from czitools import czi_metadata as czimd
+from czitools.metadata_tools import czi_metadata as czimd
 from pathlib import Path
 import pytest
 from typing import Dict
@@ -25,7 +25,7 @@
 )
 def test_instrument(czifile: str, result_mic: Dict, result_det: Dict) -> None:
 
-    # get the filepath and the metadata
+    # get the filepath and the metadata_tools
     filepath = basedir / "data" / czifile
     mic = czimd.CziMicroscope(filepath)
     det = czimd.CziDetector(filepath)
@@ -120,7 +120,7 @@ def test_instrument(czifile: str, result_mic: Dict, result_det: Dict) -> None:
 )
 def test_objectives(czifile: str, result: Dict) -> None:
 
-    # get the filepath and the metadata
+    # get the filepath and the metadata_tools
     filepath = basedir / "data" / czifile
     obj = czimd.CziObjectives(filepath)
 

src/czitools/_tests/test_md_general.py

@@ -1,4 +1,4 @@
-from czitools import czi_metadata as czimd
+from czitools.metadata_tools import czi_metadata as czimd
 from pathlib import Path
 import numpy as np
 import pytest
@@ -113,7 +113,7 @@ def test_scene_shape(czifile: str, shape: bool) -> None:
 
     assert (Path.exists(filepath) is True)
 
-    # get the complete metadata at once as one big class
+    # get the complete metadata_tools at once as one big class
     md = czimd.CziMetadata(filepath)
 
     assert (md.scene_shape_is_consistent == shape)
@@ -123,7 +123,7 @@ def test_reading_czi_fresh():
 
     filepath = basedir / r"data/A01_segSD.czi"
 
-    # get the complete metadata at once as one big class
+    # get the complete metadata_tools at once as one big class
     mdata = czimd.CziMetadata(filepath)
 
     assert (mdata.sample.well_array_names == [])

src/czitools/_tests/test_misc.py

@@ -1,5 +1,5 @@
-from czitools import read_tools
-from czitools.tools import misc
+from czitools.read_tools import read_tools
+from czitools.utils import misc
 from pathlib import Path
 import dask.array as da
 import zarr

src/czitools/_tests/test_napari_tools.py

@@ -2,16 +2,17 @@
 
 try:
     import napari
-    from czitools import napari_tools, czi_metadata
+    from czitools.napari_tools import napari_tools
+    from czitools.metadata_tools import czi_metadata
 
     NAPARI_INSTALLED = True
 except (ImportError, ModuleNotFoundError) as error:
     NAPARI_INSTALLED = False
 
 
-from czitools import read_tools
+from czitools.read_tools import read_tools
 import numpy as np
-from czitools.czi_metadata import CziMetadata
+from czitools.metadata_tools.czi_metadata import CziMetadata
 from pathlib import Path
 from typing import Dict, Tuple, Literal
 import os

src/czitools/_tests/test_read_attachments.py

@@ -1,5 +1,6 @@
-from czitools import read_tools, czi_metadata
-from czitools.read_tools import AttachmentType
+from czitools.read_tools import read_tools
+from czitools.metadata_tools import czi_metadata
+from czitools.metadata_tools.helper import AttachmentType
 from pathlib import Path
 import numpy as np
 import pytest
@@ -42,7 +43,7 @@ def test_read_attachments_images(
     has_prescan: bool,
     array_shape: Tuple[int, int, int],
 ) -> None:
-    # get the filepath and the metadata
+    # get the filepath and the metadata_tools
     filepath = basedir / "data" / cziname
 
     # get info about attachments only

src/czitools/_tests/test_read_mdarray.py

@@ -1,4 +1,4 @@
-from czitools import read_tools
+from czitools.read_tools import read_tools
 from pathlib import Path
 import dask.array as da
 import numpy as np

src/czitools/_tests/test_save_planetable.py

@@ -1,7 +1,7 @@
 import pandas as pd
 import unittest
 import os
-from czitools.tools import misc
+from czitools.utils import misc
 
 
 class TestSavePlanetTable(unittest.TestCase):

src/czitools/_tests/test_scaling.py

@@ -1,4 +1,4 @@
-from czitools import czi_metadata as czimd
+from czitools.metadata_tools import czi_metadata as czimd
 from pathlib import Path
 from box import BoxList
 import pytest
@@ -21,7 +21,7 @@
 )
 def test_scaling1(czifile: str, results: Dict) -> None:
 
-    # get the filepath and the metadata
+    # get the filepath and the metadata_tools
     filepath = basedir / "data" / czifile
     czi_scaling = czimd.CziScaling(filepath)
     out = czi_scaling.__dict__

src/czitools/_tests/test_stageXY.py

@@ -1,4 +1,4 @@
-from czitools import czi_metadata as czimd
+from czitools.metadata_tools import czi_metadata as czimd
 from pathlib import Path
 import pytest
 from typing import Dict
@@ -28,7 +28,7 @@ def test_stage_xy(czifile: str, results: Dict) -> None:
     # get the CZI filepath
     filepath = basedir / "data" / czifile
 
-    # read the metadata
+    # read the metadata_tools
     md = czimd.CziMetadata(filepath)
 
     if md.image.SizeS is not None:

src/czitools/_tests/test_writing.py

@@ -1,5 +1,7 @@
-from czitools import read_tools, write_tools, czi_metadata as czimd
-from czitools.tools import misc
+from czitools.read_tools import read_tools
+from czitools.write_tools import write_tools
+from czitools.metadata_tools import czi_metadata as czimd
+from czitools.utils import misc
 from pylibCZIrw import czi as pyczi
 import shutil
 from pathlib import Path
@@ -96,7 +98,7 @@ def test_write_2(
             # write the plane with shape (Y, X, 1) to the new CZI file
             czidoc_w.write(data=mdarray[0, 0, ch, z, ...], plane={"C": ch, "Z": z})
 
-    # get the complete metadata at once as one big class
+    # get the complete metadata_tools at once as one big class
     mdata = czimd.CziMetadata(newczi)
 
     assert mdata.pyczi_dims == pyczi_dims
@@ -152,7 +154,7 @@ def test_write_3(
             # change the x-position for the next round to write "side-by-side"
             xstart = xstart + 512
 
-    # get the complete metadata at once as one big class
+    # get the complete metadata_tools at once as one big class
     mdata = czimd.CziMetadata(newczi_zloc)
 
     assert mdata.pyczi_dims == pyczi_dims
@@ -224,7 +226,7 @@ def test_write_4(
                 location=(locx[z], locy[z]),
             )
 
-        # get the complete metadata at once as one big class
+        # get the complete metadata_tools at once as one big class
     mdata = czimd.CziMetadata(newczi_zscenes)
 
     assert mdata.pyczi_dims == pyczi_dims