update TransformationMeta import from iohub.ngff_meta to iohub.ngff

czbiohub-sf · Sep 18, 2024 · 8e8c144 · 8e8c144
1 parent e277ccf
commit 8e8c144
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Showing 6 changed files with 6 additions and 9 deletions.
diff --git a/mantis/acquisition/scripts/measure_psf.py b/mantis/acquisition/scripts/measure_psf.py
@@ -7,7 +7,7 @@
 import numpy as np
 import torch
 
-from iohub.ngff_meta import TransformationMeta
+from iohub.ngff import TransformationMeta
 from iohub.reader import open_ome_zarr
 from pycromanager import Acquisition, Core, multi_d_acquisition_events
 

diff --git a/mantis/analysis/scripts/simple_phase_recon.py b/mantis/analysis/scripts/simple_phase_recon.py
@@ -4,7 +4,7 @@
 import numpy as np
 
 from iohub import open_ome_zarr, read_micromanager
-from iohub.ngff_meta import TransformationMeta
+from iohub.ngff import TransformationMeta
 from recOrder.compute.reconstructions import initialize_reconstructor, reconstruct_phase3D
 
 # %% Load data

diff --git a/mantis/cli/estimate_psf.py b/mantis/cli/estimate_psf.py
@@ -8,8 +8,7 @@
 import numpy as np
 import torch
 
-from iohub.ngff import open_ome_zarr
-from iohub.ngff_meta import TransformationMeta
+from iohub.ngff import open_ome_zarr, TransformationMeta
 
 from mantis.analysis.AnalysisSettings import PsfFromBeadsSettings
 from mantis.analysis.analyze_psf import detect_peaks, extract_beads

diff --git a/mantis/cli/stitch.py b/mantis/cli/stitch.py
@@ -8,8 +8,7 @@
 import numpy as np
 import pandas as pd
 
-from iohub import open_ome_zarr
-from iohub.ngff_meta import TransformationMeta
+from iohub import open_ome_zarr, TransformationMeta
 from slurmkit import HAS_SLURM, SlurmParams, slurm_function, submit_function
 
 from mantis.analysis.AnalysisSettings import StitchSettings

diff --git a/mantis/cli/update_scale_metadata.py b/mantis/cli/update_scale_metadata.py
@@ -3,7 +3,7 @@
 import click
 
 from iohub import open_ome_zarr
-from iohub.ngff_meta import TransformationMeta
+from iohub.ngff import TransformationMeta
 
 from mantis.cli.parsing import input_position_dirpaths
 

diff --git a/mantis/cli/utils.py b/mantis/cli/utils.py
@@ -12,8 +12,7 @@
 import numpy as np
 import yaml
 
-from iohub.ngff import Position, open_ome_zarr
-from iohub.ngff_meta import TransformationMeta
+from iohub.ngff import Position, open_ome_zarr, TransformationMeta
 from numpy.typing import DTypeLike
 from tqdm import tqdm