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Don't let OME t_scale be equal to zero (#361)
* don't set t_scale to 0.0 * reformat z_step=0 warning
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iohub/mmstack.py

Lines changed: 13 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -247,20 +247,24 @@ def _set_mm_meta(self, mm_meta: dict) -> None:
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for ch in self._mm_meta["Summary"].get("ChNames", []):
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self.channel_names.append(ch)
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z_step_size = float(self._mm_meta["Summary"].get("z-step_um", 1.0))
250-
if z_step_size == 0:
251-
if self.slices == 1:
252-
z_step_size = 1.0
253-
else:
250+
if z_step_size == 0.0:
251+
z_step_size = 1.0
252+
if self.slices != 1:
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_logger.warning(
255-
f"Z-step size is {z_step_size} um in the metadata, "
256-
"Using 1.0 um instead."
254+
"Z-step size is set to 0.0 um in the metadata, "
255+
"using 1.0 um instead."
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)
258257
self._z_step_size = z_step_size
259258
self.height = self._mm_meta["Summary"]["Height"]
260259
self.width = self._mm_meta["Summary"]["Width"]
261-
self._t_scale = (
262-
float(self._mm_meta["Summary"].get("Interval_ms", 1e3)) / 1e3
263-
)
260+
t_scale = float(self._mm_meta["Summary"].get("Interval_ms", 1e3)) / 1e3
261+
if t_scale == 0.0:
262+
t_scale = 1.0
263+
_logger.warning(
264+
"Time scale is set to 0.0 in the metadata, "
265+
"using 1.0 instead."
266+
)
267+
self._t_scale = t_scale
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265269
def _simplify_stage_position(self, stage_pos: dict):
266270
"""

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