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More robust calculation of "z-step_um" for ndtiff datasets #263

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Dec 11, 2024
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More robust calculation of "z-step_um" for ndtiff datasets #263

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23 changes: 12 additions & 11 deletions iohub/ndtiff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -140,19 +140,20 @@ def _get_summary_metadata(self):
c_idx = self._ndtiff_channel_names[0]
img_metadata = self.get_image_metadata(p_idx, 0, c_idx, 0)

pm_metadata["z-step_um"] = None
if "ZPosition_um_Intended" in img_metadata.keys():
try:
z0 = self.get_image_metadata(p_idx, 0, c_idx, 0)[
"ZPosition_um_Intended"
]
z1 = self.get_image_metadata(p_idx, 0, c_idx, 1)[
"ZPosition_um_Intended"
]
pm_metadata["z-step_um"] = np.around(
abs(
self.get_image_metadata(p_idx, 0, c_idx, 1)[
"ZPosition_um_Intended"
]
- self.get_image_metadata(p_idx, 0, c_idx, 0)[
"ZPosition_um_Intended"
]
),
decimals=3,
abs(z1 - z0), decimals=3
).astype(float)
# Will raise KeyError if dataset does not have z slices
# Will raise ValueError if dataset has only one z slice
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except (KeyError, ValueError):
pm_metadata["z-step_um"] = None

pm_metadata["StagePositions"] = []
if "position" in self._axes:
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