From 8e8c1440822c8029d205e966bcafa61e4a197a19 Mon Sep 17 00:00:00 2001
From: Taylla Milena Theodoro <taylla.theodoro@gpu-e-3.clusternet>
Date: Wed, 18 Sep 2024 10:45:34 -0700
Subject: [PATCH] update TransformationMeta import from iohub.ngff_meta to
 iohub.ngff

---
 mantis/acquisition/scripts/measure_psf.py     | 2 +-
 mantis/analysis/scripts/simple_phase_recon.py | 2 +-
 mantis/cli/estimate_psf.py                    | 3 +--
 mantis/cli/stitch.py                          | 3 +--
 mantis/cli/update_scale_metadata.py           | 2 +-
 mantis/cli/utils.py                           | 3 +--
 6 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/mantis/acquisition/scripts/measure_psf.py b/mantis/acquisition/scripts/measure_psf.py
index 5584f5be..0ba63cdb 100644
--- 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
index 54360191..e22eb3ae 100644
--- 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
index 7c99b441..dc31c645 100644
--- 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
index 4d26ff36..78eaa478 100644
--- 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
index 0fc19989..7b33c7fc 100644
--- 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
index d244799e..c7e39388 100644
--- 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