Merge pull request #28 from sebi06/work_in_progress

Work in progress

README.md

@@ -32,7 +32,7 @@ xmlfile = czimd.writexml(filepath)
 czi_channels = czimd.CziChannelInfo(filepath)
 
 # get the complete metadata from the CZI as one big object
-czimd_complete = czimd.CziMetadataComplete(filepath)
+czimd_complete = czimd.get_metadata_as_object(filepath)
 
 # get an object containing only the dimension information
 czi_dimensions = czimd.CziDimensions(filepath)

demo/notebooks/save_with_ZSTD_compression.ipynb

@@ -144,9 +144,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python [conda env:ia39]",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "conda-env-ia39-py"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -158,7 +158,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.10.8"
   },
   "vscode": {
    "interpreter": {

demo/scripts/use_pylibczirw_metadata_class.py

@@ -43,7 +43,7 @@
 czi_channels = czimd.CziChannelInfo(filepath)
 
 # get the complete metadata from the CZI as one big object
-czimd_complete = czimd.CziMetadataComplete(filepath)
+czimd_complete = czimd.get_metadata_as_object(filepath)
 
 # get an object containing only the dimension information
 czi_dimensions = czimd.CziDimensions(filepath)

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = czitools
-version = 0.2.0
+version = 0.2.1
 author = Sebastian Rhode
 author_email = [email protected]
 url = https://github.com/sebi06/czitools

src/czitools/__init__.py

@@ -1,3 +1,3 @@
 # __init__.py
 # version of the czitools package
-__version__ = "0.2.0"
+__version__ = "0.2.1"

src/czitools/_tests/test_channelinfo.py

@@ -1,38 +1,43 @@
 from pathlib import Path
 from czitools import pylibczirw_metadata as czimd
-
-basedir = Path(__file__).resolve().parents[3]
-
-
-def test_channelinfo():
-
-    # get the CZI filepath
-    filepath = basedir / r"data/CellDivision_T=3_Z=5_CH=2_X=240_Y=170.czi"
-    czi_channels = czimd.CziChannelInfo(filepath)
-
-    assert (czi_channels.clims == [[0.0, 0.05983062485694667], [0.0, 0.24975967040512703]])
-    assert (czi_channels.colors == ["#FFFF7E00", "#FF00FF33"])
-    assert (czi_channels.gamma == [0.7999999999999998, 0.7999999999999998])
-    assert (czi_channels.names == ["LED555", "LED470"])
-    assert (czi_channels.dyes == ["AF555", "AF488"])
-
-    # get the CZI filepath
-    filepath = basedir / r"data/Al2O3_SE_020_sp.czi"
-    czi_channels = czimd.CziChannelInfo(filepath)
-
-    assert (czi_channels.clims == [[0.0, 0.5]])
-    assert (czi_channels.colors == ["#80808000"])
-    assert (czi_channels.gamma == [0.85])
-    assert (czi_channels.names == ["CH1"])
-    assert (czi_channels.dyes == ["Dye-CH1"])
+import pytest
+from typing import List, Dict, Tuple, Optional, Type, Any, Union, Mapping
+
+basedir = Path(__file__).resolve().parents[3] / "data"
+
+@pytest.mark.parametrize(
+    "czifile, clims, colors, gamma, names, dyes",
+        [
+            ("CellDivision_T=3_Z=5_CH=2_X=240_Y=170.czi",
+             [[0.0, 0.05983062485694667],[0.0, 0.24975967040512703]],
+             ["#FFFF7E00", "#FF00FF33"],
+             [0.7999999999999998, 0.7999999999999998],
+             ["LED555", "LED470"],
+             ["AF555", "AF488"]),
+
+            ("Al2O3_SE_020_sp.czi",
+             [[0.0, 0.5]],
+             ["#80808000"],
+             [0.85],
+             ["CH1"],
+             ["Dye-CH1"]),
+
+            ("w96_A1+A2.czi",
+             [[0.000871455799315693, 0.044245974575704575], [0.000881881329185286, 0.05011349562051524]],
+             ['#FFFF1800', '#FF00FF33'],
+             [0.7999999999999998, 0.7999999999999998],
+             ['AF568', 'AF488'],
+             ['AF568', 'AF488'])
+        ]
+)
+def test_channelinfo(czifile: str, clims: List, colors: List, gamma: List, names: List, dyes: List) -> None:
 
     # get the CZI filepath
-    filepath = basedir / r"data/w96_A1+A2.czi"
+    filepath = basedir / czifile
     czi_channels = czimd.CziChannelInfo(filepath)
 
-    assert (czi_channels.clims == [[0.000871455799315693, 0.044245974575704575], [
-            0.000881881329185286, 0.05011349562051524]])
-    assert (czi_channels.colors == ['#FFFF1800', '#FF00FF33'])
-    assert (czi_channels.gamma == [0.7999999999999998, 0.7999999999999998])
-    assert (czi_channels.names == ['AF568', 'AF488'])
-    assert (czi_channels.dyes == ['AF568', 'AF488'])
+    assert (czi_channels.clims == clims)
+    assert (czi_channels.colors == colors)
+    assert (czi_channels.gamma == gamma)
+    assert (czi_channels.names == names)
+    assert (czi_channels.dyes == dyes)

src/czitools/_tests/test_czimd_box.py

@@ -1,62 +1,68 @@
 from czitools import pylibczirw_metadata as czimd
 from pathlib import Path, PurePath
+import pytest
+from typing import List, Dict, Tuple, Optional, Type, Any, Union, Mapping
 
 
 # adapt to your needs
 defaultdir = Path(__file__).resolve().parents[3] / "data"
 
-def test_general_attr():
+
+@pytest.mark.parametrize(
+    "attribute",
+    [
+        "has_customattr",
+        "has_exp",
+        "has_disp",
+        "has_hardware",
+        "has_scale",
+        "has_instrument",
+        "has_microscopes",
+        "has_detectors",
+        "has_objectives",
+        "has_tubelenses",
+        "has_disp",
+        "has_channels",
+        "has_info",
+        "has_app",
+        "has_doc",
+        "has_image",
+        "has_scenes",
+        "has_dims"
+    ]
+)
+def test_general_attr(attribute: str) -> None:
 
     filepath = defaultdir / "CellDivision_T=3_Z=5_CH=2_X=240_Y=170.czi"
 
     czibox = czimd.get_czimd_box(filepath)
 
-    assert(hasattr(czibox, "has_customattr"))
-    assert(hasattr(czibox, "has_exp = False"))
-    assert(hasattr(czibox, "has_disp"))
-    assert(hasattr(czibox, "has_hardware"))
-    assert(hasattr(czibox, "has_scale"))
-    assert(hasattr(czibox, "has_instrument"))
-    assert(hasattr(czibox, "has_microscopes"))
-    assert(hasattr(czibox, "has_detectors"))
-    assert(hasattr(czibox, "has_objectives"))
-    assert(hasattr(czibox, "has_tubelenses"))
-    assert(hasattr(czibox, "has_disp"))
-    assert(hasattr(czibox, "has_channels"))
-    assert(hasattr(czibox, "has_info"))
-    assert(hasattr(czibox, "has_app"))
-    assert(hasattr(czibox, "has_doc"))
-    assert(hasattr(czibox, "has_image"))
-    assert(hasattr(czibox, "has_scenes"))
-    assert(hasattr(czibox, "has_dims"))
-
-
-def test_box():
-
-    czifiles = ["CellDivision_T=3_Z=5_CH=2_X=240_Y=170.czi",
-                "Al2O3_SE_020_sp.czi",
-                "w96_A1+A2.czi",
-                "Airyscan.czi",
-                "newCZI_zloc.czi",
-                "does_not_exist.czi",
-                "FOV7_HV110_P0500510000.czi",
-                "Tumor_HE_RGB.czi",
-                "WP96_4Pos_B4-10_DAPI.czi",
-                "S=3_1Pos_2Mosaic_T=2=Z=3_CH=2_sm.czi"
-                ]
-
-    results = [True, True, True, True, True, False, True, True, True, True]
-
-    for czifile, result in zip(czifiles, results):
-
-        filepath = defaultdir / czifile
-
-        try:
-            czibox = czimd.get_czimd_box(filepath)
-            ok = True
-        except Exception:
-            ok = False
-
-        assert(ok == result)
-
-test_box()
+    assert (hasattr(czibox, attribute))
+
+
+@pytest.mark.parametrize(
+    "czifile, expected",
+    [
+        ("CellDivision_T=3_Z=5_CH=2_X=240_Y=170.czi", True),
+        ("Al2O3_SE_020_sp.czi", True),
+        ("w96_A1+A2.czi", True),
+        ("Airyscan.czi", True),
+        ("newCZI_zloc.czi", True),
+        ("does_not_exist.czi", False),
+        ("FOV7_HV110_P0500510000.czi", True),
+        ("Tumor_HE_RGB.czi", True),
+        ("WP96_4Pos_B4-10_DAPI.czi", True),
+        ("S=3_1Pos_2Mosaic_T=2=Z=3_CH=2_sm.czi", True)
+    ]
+)
+def test_box(czifile: List[str], expected: bool) -> None:
+
+    filepath = defaultdir / czifile
+
+    try:
+        czibox = czimd.get_czimd_box(filepath)
+        ok = True
+    except Exception:
+        ok = False
+
+    assert (ok == expected)

src/czitools/_tests/test_dimensions.py

@@ -1,14 +1,20 @@
 
 from czitools import pylibczirw_metadata as czimd
 from pathlib import Path
+import pytest
+from typing import List, Dict, Tuple, Optional, Type, Any, Union, Mapping
 
 basedir = Path(__file__).resolve().parents[3]
 
-# get the CZI filepath
-filepath = basedir / r"data/CellDivision_T=3_Z=5_CH=2_X=240_Y=170.czi"
+@pytest.mark.parametrize(
+    "czifile, dimension",
+    [
+        ("CellDivision_T=3_Z=5_CH=2_X=240_Y=170.czi", [None, 3, 5, 2, 170, 240])
+    ]
+)
+def test_dimensions(czifile: str, dimension: List[Any]) -> None:
 
-
-def test_dimensions():
+    filepath = basedir / "data" / czifile
 
     czi_dimensions = czimd.CziDimensions(filepath)
     print("SizeS: ", czi_dimensions.SizeS)
@@ -18,9 +24,9 @@ def test_dimensions():
     print("SizeY: ", czi_dimensions.SizeY)
     print("SizeX: ", czi_dimensions.SizeX)
 
-    assert (czi_dimensions.SizeS is None)
-    assert (czi_dimensions.SizeT == 3)
-    assert (czi_dimensions.SizeZ == 5)
-    assert (czi_dimensions.SizeC == 2)
-    assert (czi_dimensions.SizeY == 170)
-    assert (czi_dimensions.SizeX == 240)
+    assert (czi_dimensions.SizeS == dimension[0])
+    assert (czi_dimensions.SizeT == dimension[1])
+    assert (czi_dimensions.SizeZ == dimension[2])
+    assert (czi_dimensions.SizeC == dimension[3])
+    assert (czi_dimensions.SizeY == dimension[4])
+    assert (czi_dimensions.SizeX == dimension[5])

src/czitools/_tests/test_info.py

@@ -1,43 +1,40 @@
 from czitools import pylibczirw_metadata as czimd
 from pathlib import Path
+import pytest
+from typing import List, Dict, Tuple, Optional, Type, Any, Union, Mapping
 
 basedir = Path(__file__).resolve().parents[3]
 
 
-def test_information():
-
-    to_test = {0: r"data/CellDivision_T=3_Z=5_CH=2_X=240_Y=170.czi",
-               1: r"data/Airyscan.czi",
-               2: r"data/newCZI_zloc.czi"}
-
-    results = {0: ['ZEN 3.2 (blue edition)',
-                   '3.2.0.00001',
-                   '2016-02-12T09:41:02.4915604Z',
-                   True,
-                   'CellDivision_T=3_Z=5_CH=2_X=240_Y=170.czi'],
-               1: ['ZEN (blue edition)',
-                   '3.5.093.00000',
-                   None,
-                   True,
-                   'Airyscan.czi'],
-               2: ['pylibCZIrw',
-                   '3.2.1',
-                   None,
-                   True,
-                   'newCZI_zloc.czi']
-               }
-
-    for t in range(len(to_test)):
-
-        # get the filepath
-        filepath = basedir / to_test[t]
-        md = czimd.CziMetadata(filepath)
-
-        assert (md.software_name == results[t][0])
-        assert (md.software_version == results[t][1])
-        assert (md.acquisition_date == results[t][2])
-        assert (Path.exists(Path(md.dirname)) == results[t][3])
-        assert (md.filename == results[t][4])
-
-
-test_information()
+@pytest.mark.parametrize(
+    "czifile, result",
+    [
+        ("CellDivision_T=3_Z=5_CH=2_X=240_Y=170.czi", ['ZEN 3.2 (blue edition)',
+                                                             '3.2.0.00001',
+                                                             '2016-02-12T09:41:02.4915604Z',
+                                                             True,
+                                                             'CellDivision_T=3_Z=5_CH=2_X=240_Y=170.czi']),
+        
+        ("Airyscan.czi", ['ZEN (blue edition)',
+                                '3.5.093.00000',
+                                None,
+                                True,
+                                'Airyscan.czi']),
+        
+        ("newCZI_zloc.czi", ['pylibCZIrw',
+                                   '3.2.1',
+                                   None,
+                                   True,
+                                   'newCZI_zloc.czi'])
+    ]
+)
+def test_information(czifile: str, result: List) -> None:
+
+    filepath = basedir / "data" / czifile
+    md = czimd.CziMetadata(filepath)
+
+    assert (md.software_name == result[0])
+    assert (md.software_version == result[1])
+    assert (md.acquisition_date == result[2])
+    assert (Path.exists(Path(md.dirname)) == result[3])
+    assert (md.filename == result[4])