fix issue with reading too many planes

sebi06 · sebi06 · commit 86fde1ba1816 · 2025-11-09T21:12:32.000+01:00
diff --git a/demo/omezarr_testing/write_omezarr_ngff.py b/demo/omezarr_testing/write_omezarr_ngff.py
@@ -6,7 +6,7 @@
 # Point to the main data folder (two directories up from demo/omezarr_testing)
 filepath1: str = str(Path(__file__).parent.parent.parent / "data" / "CellDivision_T10_Z15_CH2_DCV_small.czi")
 filepath2: str = str(Path(__file__).parent.parent.parent / "data" / "WP96_4Pos_B4-10_DAPI.czi")
-filepaths = [filepath1, filepath2]
+filepaths = [Path(filepath1), Path(filepath2)]
 
 show_napari = False  # Whether to display the result in napari viewer
 
diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = czitools
-version = 0.11.1
+version = 0.11.2
 author = Sebastian Rhode
 author_email = sebrhode@gmail.com
 url = https://github.com/sebi06/czitools
diff --git a/src/czitools/metadata_tools/sample.py b/src/czitools/metadata_tools/sample.py
@@ -115,7 +115,7 @@ def __post_init__(self):
             try:
                 # read the data from CSV file from a single plane
                 planetable, savepath = get_planetable(
-                    czi_box.filepath, {"scene": 0, "tile": 0, "time": 0, "channel": 0, "zplane": 0}
+                    czi_box.filepath, planes={"scene": 0, "tile": 0, "time": 0, "channel": 0, "zplane": 0}
                 )
 
                 self.image_stageX = float(planetable["X[micron]"][0])

Original file line number	Diff line number	Diff line change
`@@ -115,7 +115,7 @@ def __post_init__(self):`
`115`	`115`	`try:`
`116`	`116`	`# read the data from CSV file from a single plane`
`117`	`117`	`planetable, savepath = get_planetable(`
`118`		`- czi_box.filepath, {"scene": 0, "tile": 0, "time": 0, "channel": 0, "zplane": 0}`
	`118`	`+ czi_box.filepath, planes={"scene": 0, "tile": 0, "time": 0, "channel": 0, "zplane": 0}`
`119`	`119`	`)`
`120`	`120`
`121`	`121`	`self.image_stageX = float(planetable["X[micron]"][0])`