ziw-liu · May 30, 2023 · May 30, 2023
diff --git a/scripts/test_zarr_reading.py b/scripts/test_zarr_reading.py
@@ -13,8 +13,8 @@
 import glob
 import time
 
-import micro_dl.utils.aux_utils as aux_utils
-import micro_dl.cli.preprocess_script as preprocess_script
+import viscy.utils.aux_utils as aux_utils
+import viscy.cli.preprocess_script as preprocess_script
 
 def parse_args():
     """Parse command line arguments

diff --git a/scripts/visualize_data_augmentation.py b/scripts/visualize_data_augmentation.py
@@ -14,9 +14,9 @@
 sys.path.insert(0, "/home/shalin.mehta/code/microDL")
 
 import microDL.micro_dl.training.training as training
-import micro_dl.utils.aux_utils as aux_utils
+import viscy.utils.aux_utils as aux_utils
 import microDL.micro_dl.utils.cli_utils as torch_io_utils
-import micro_dl.plotting.plot_utils as plot_utils
+import viscy.plotting.plot_utils as plot_utils
 
 
 def visualize_dataloading(

diff --git a/tests/cli/inference_script_tests.py b/tests/cli/inference_script_tests.py
@@ -8,8 +8,8 @@
 from unittest.mock import patch
 import yaml
 
-import micro_dl.cli.inference_script as inference_script
-import micro_dl.utils.aux_utils as aux_utils
+import viscy.cli.inference_script as inference_script
+import viscy.utils.aux_utils as aux_utils
 
 
 class TestInferenceScript(unittest.TestCase):

diff --git a/tests/cli/metrics_script_tests.py b/tests/cli/metrics_script_tests.py
@@ -8,9 +8,9 @@
 from unittest.mock import patch
 import yaml
 
-import micro_dl.cli.metrics_script as metrics_script
-import micro_dl.utils.aux_utils as aux_utils
-import micro_dl.utils.normalize as normalize
+import viscy.cli.metrics_script as metrics_script
+import viscy.utils.aux_utils as aux_utils
+import viscy.utils.normalize as normalize
 
 
 class TestMetricsScript(unittest.TestCase):

diff --git a/tests/cli/preprocess_script_test.py b/tests/cli/preprocess_script_test.py
@@ -5,9 +5,9 @@
 from testfixtures import TempDirectory
 import unittest
 
-import micro_dl.cli.preprocess_script as pp
-import micro_dl.utils.aux_utils as aux_utils
-import micro_dl.utils.io_utils as io_utils
+import viscy.cli.preprocess_script as pp
+import viscy.utils.aux_utils as aux_utils
+import viscy.utils.io_utils as io_utils
 
 
 class TestPreprocessScript(unittest.TestCase):

diff --git a/tests/evaluation/evaluation_metrics_tests.py b/tests/evaluation/evaluation_metrics_tests.py
@@ -1,7 +1,7 @@
 import nose.tools
 import numpy as np
 
-import micro_dl.evaluation.evaluation_metrics as metrics
+import viscy.evaluation.evaluation_metrics as metrics
 
 
 im_shape = (35, 45, 25)

diff --git a/tests/input/dataset_tests.py b/tests/input/dataset_tests.py
@@ -5,7 +5,7 @@
 from testfixtures import TempDirectory
 import unittest
 
-import micro_dl.input.transformations as transformations
+import viscy.input.transformations as transformations
 
 
 class TestBaseDataSet(unittest.TestCase):

diff --git a/tests/input/dataset_with_mask_tests.py b/tests/input/dataset_with_mask_tests.py
@@ -5,7 +5,7 @@
 from testfixtures import TempDirectory
 import unittest
 
-import micro_dl.input.dataset_with_mask as dataset_mask
+import viscy.input.dataset_with_mask as dataset_mask
 
 
 class TestDataSetWithMask(unittest.TestCase):

diff --git a/tests/input/inference_dataset_tests.py b/tests/input/inference_dataset_tests.py
@@ -4,8 +4,8 @@
 from testfixtures import TempDirectory
 import unittest
 
-import micro_dl.inference.inference_dataset as inference_dataset
-import micro_dl.utils.aux_utils as aux_utils
+import viscy.inference.inference_dataset as inference_dataset
+import viscy.utils.aux_utils as aux_utils
 
 
 class TestInferenceDataSet(unittest.TestCase):

diff --git a/tests/networks/conv_blocks_tests.py b/tests/networks/conv_blocks_tests.py
@@ -6,9 +6,9 @@
 import numpy as np
 import unittest
 
-from micro_dl.networks import conv_blocks as conv_blocks
-from micro_dl.utils.aux_utils import get_channel_axis
-from micro_dl.utils.network_utils import get_keras_layer
+from viscy.networks import conv_blocks as conv_blocks
+from viscy.utils.aux_utils import get_channel_axis
+from viscy.utils.network_utils import get_keras_layer
 
 
 class TestConvBlocks(unittest.TestCase):

diff --git a/tests/networks/image2D_to_vector_net_tests.py b/tests/networks/image2D_to_vector_net_tests.py
@@ -5,7 +5,7 @@
 import numpy as np
 import unittest
 
-from micro_dl.networks import Image2DToVectorNet
+from viscy.networks import Image2DToVectorNet
 
 
 class TestImage2DToVectorNet(unittest.TestCase):

diff --git a/tests/networks/image3D_to_vector_net_tests.py b/tests/networks/image3D_to_vector_net_tests.py
@@ -4,7 +4,7 @@
 import numpy as np
 import unittest
 
-from micro_dl.networks import Image3DToVectorNet
+from viscy.networks import Image3DToVectorNet
 
 
 class TestImage3DToVectorNet(unittest.TestCase):

diff --git a/tests/networks/unet2D_tests.py b/tests/networks/unet2D_tests.py
@@ -5,7 +5,7 @@
 import numpy as np
 import unittest
 
-from micro_dl.networks import UNet2D
+from viscy.networks import UNet2D
 
 
 class TestUNet2D(unittest.TestCase):

diff --git a/tests/networks/unet3D_tests.py b/tests/networks/unet3D_tests.py
@@ -6,7 +6,7 @@
 import numpy as np
 from keras import Model
 
-from micro_dl.networks import UNet3D
+from viscy.networks import UNet3D
 
 
 class TestUNet3D(unittest.TestCase):

diff --git a/tests/networks/unet_stack_2D_tests.py b/tests/networks/unet_stack_2D_tests.py
@@ -5,7 +5,7 @@
 import numpy as np
 import unittest
 
-from micro_dl.networks import UNetStackTo2D
+from viscy.networks import UNetStackTo2D
 
 
 class TestUNetStackTo2D(unittest.TestCase):

diff --git a/tests/networks/unet_stack_to_stack_tests.py b/tests/networks/unet_stack_to_stack_tests.py
@@ -6,7 +6,7 @@
 import numpy as np
 import unittest
 
-from micro_dl.networks import UNetStackToStack
+from viscy.networks import UNetStackToStack
 
 
 class TestUNetStackToStack(unittest.TestCase):

diff --git a/tests/plotting/plot_utils_tests.py b/tests/plotting/plot_utils_tests.py
@@ -5,7 +5,7 @@
 import os
 from testfixtures import TempDirectory
 
-import micro_dl.plotting.plot_utils as plot_utils
+import viscy.plotting.plot_utils as plot_utils
 
 
 def test_save_predicted_images():

diff --git a/tests/preprocessing/generate_masks_tests.py b/tests/preprocessing/generate_masks_tests.py
@@ -8,8 +8,8 @@
 import unittest
 import warnings
 
-from micro_dl.utils import aux_utils as aux_utils
-from micro_dl.preprocessing.generate_masks import MaskProcessor
+from viscy.utils import aux_utils as aux_utils
+from viscy.preprocessing.generate_masks import MaskProcessor
 
 
 class TestMaskProcessor(unittest.TestCase):

diff --git a/tests/preprocessing/resize_images_tests.py b/tests/preprocessing/resize_images_tests.py
@@ -6,8 +6,8 @@
 from testfixtures import TempDirectory
 import unittest
 
-import micro_dl.preprocessing.resize_images as resize_images
-import micro_dl.utils.aux_utils as aux_utils
+import viscy.preprocessing.resize_images as resize_images
+import viscy.utils.aux_utils as aux_utils
 
 
 class TestResizeImages(unittest.TestCase):

diff --git a/tests/torch_unet/networks/Unet25D_tests.py b/tests/torch_unet/networks/Unet25D_tests.py
@@ -4,8 +4,8 @@
 import itertools
 import unittest
 
-from micro_dl.torch_unet.networks.Unet25D import Unet25d
-import micro_dl.utils.cli_utils as io_utils
+from viscy.torch_unet.networks.Unet25D import Unet25d
+import viscy.utils.cli_utils as io_utils
 
 
 class TestUnet25d(unittest.TestCase):

diff --git a/tests/torch_unet/networks/Unet2D_tests.py b/tests/torch_unet/networks/Unet2D_tests.py
@@ -4,8 +4,8 @@
 import itertools
 import unittest
 
-from micro_dl.torch_unet.networks.Unet2D import Unet2d
-import micro_dl.utils.cli_utils as io_utils
+from viscy.torch_unet.networks.Unet2D import Unet2d
+import viscy.utils.cli_utils as io_utils
 
 
 class TestUnet2d(unittest.TestCase):

diff --git a/tests/torch_unet/networks/layers/ConvBlock2D_tests.py b/tests/torch_unet/networks/layers/ConvBlock2D_tests.py
@@ -4,8 +4,8 @@
 import itertools
 import unittest
 
-from micro_dl.torch_unet.networks.layers.ConvBlock2D import ConvBlock2D
-import micro_dl.utils.cli_utils as io_utils
+from viscy.torch_unet.networks.layers.ConvBlock2D import ConvBlock2D
+import viscy.utils.cli_utils as io_utils
 
 
 class TestConvBlock2D(unittest.TestCase):

diff --git a/tests/torch_unet/networks/layers/ConvBlock3D_tests.py b/tests/torch_unet/networks/layers/ConvBlock3D_tests.py
@@ -4,8 +4,8 @@
 import itertools
 import unittest
 
-from micro_dl.torch_unet.networks.layers.ConvBlock3D import ConvBlock3D
-import micro_dl.utils.cli_utils as io_utils
+from viscy.torch_unet.networks.layers.ConvBlock3D import ConvBlock3D
+import viscy.utils.cli_utils as io_utils
 
 
 class TestConvBlock3D(unittest.TestCase):

diff --git a/tests/torch_unet/utils/dataset_tests.py b/tests/torch_unet/utils/dataset_tests.py
@@ -14,9 +14,9 @@
 
 sys.path.insert(0, "/home/christian.foley/virtual_staining/workspaces/microDL")
 
-import micro_dl.torch_unet.utils.dataset as dataset_utils
-import micro_dl.utils.io_utils as io_utils
-import micro_dl.cli.preprocess_script as preprocess_script
+import viscy.torch_unet.utils.dataset as dataset_utils
+import viscy.utils.io_utils as io_utils
+import viscy.cli.preprocess_script as preprocess_script
 
 
 class TestDataset(unittest.TestCase):

diff --git a/tests/torch_unet/utils/training_tests.py b/tests/torch_unet/utils/training_tests.py
@@ -11,8 +11,8 @@
 import unittest
 
 
-from micro_dl.input.dataset import ToTensor
-from micro_dl.training.training import TorchTrainer
+from viscy.input.dataset import ToTensor
+from viscy.training.training import TorchTrainer
 from tests.torch_unet.utils.dataset_tests import TestDataset
 
 

diff --git a/tests/utils/aux_utils_tests.py b/tests/utils/aux_utils_tests.py
@@ -6,7 +6,7 @@
 import os
 from testfixtures import TempDirectory
 
-import micro_dl.utils.aux_utils as aux_utils
+import viscy.utils.aux_utils as aux_utils
 
 
 # Create test metadata table

diff --git a/tests/utils/image_utils_tests.py b/tests/utils/image_utils_tests.py
@@ -8,10 +8,10 @@
 
 # Create a test image and its corresponding coordinates and values
 # Create a test image with a bright block to the right
-import micro_dl.utils.aux_utils as aux_utils
-import micro_dl.utils.image_utils as image_utils
-import micro_dl.utils.io_utils as io_utils
-import micro_dl.utils.normalize as normalize
+import viscy.utils.aux_utils as aux_utils
+import viscy.utils.image_utils as image_utils
+import viscy.utils.io_utils as io_utils
+import viscy.utils.normalize as normalize
 from tests.utils.masks_utils_tests import uni_thr_tst_image
 
 test_im = np.zeros((10, 15), np.uint16) + 100

diff --git a/tests/utils/io_utils_tests.py b/tests/utils/io_utils_tests.py
@@ -5,7 +5,7 @@
 import unittest
 import zarr
 
-import micro_dl.utils.io_utils as io_utils
+import viscy.utils.io_utils as io_utils
 
 
 class TestZarrReader(unittest.TestCase):

diff --git a/tests/utils/masks_utils_tests.py b/tests/utils/masks_utils_tests.py
@@ -3,7 +3,7 @@
 from skimage import draw
 from skimage.filters import gaussian
 
-import micro_dl.utils.masks as masks_utils
+import viscy.utils.masks as masks_utils
 
 
 uni_thr_tst_image = np.zeros((31, 31))

diff --git a/tests/utils/meta_utils_tests.py b/tests/utils/meta_utils_tests.py
@@ -6,8 +6,8 @@
 from testfixtures import TempDirectory
 import unittest
 
-import micro_dl.utils.aux_utils as aux_utils
-import micro_dl.utils.meta_utils as meta_utils
+import viscy.utils.aux_utils as aux_utils
+import viscy.utils.meta_utils as meta_utils
 
 
 class TestMetaUtils(unittest.TestCase):

diff --git a/tests/utils/mp_utils_tests.py b/tests/utils/mp_utils_tests.py
@@ -10,11 +10,11 @@
 import unittest
 import warnings
 
-import micro_dl.utils.aux_utils as aux_utils
-import micro_dl.utils.mp_utils as mp_utils
-import micro_dl.utils.image_utils as image_utils
+import viscy.utils.aux_utils as aux_utils
+import viscy.utils.mp_utils as mp_utils
+import viscy.utils.image_utils as image_utils
 
-from micro_dl.utils.masks import create_otsu_mask
+from viscy.utils.masks import create_otsu_mask
 
 
 class TestMpUtilsBaseClass(unittest.TestCase):

diff --git a/tests/utils/preprocess_utils_tests.py b/tests/utils/preprocess_utils_tests.py
@@ -4,8 +4,8 @@
 from testfixtures import TempDirectory
 import unittest
 
-import micro_dl.utils.aux_utils as aux_utils
-import micro_dl.utils.preprocess_utils as preprocess_utils
+import viscy.utils.aux_utils as aux_utils
+import viscy.utils.preprocess_utils as preprocess_utils
 
 
 class TestPreprocessUtils(unittest.TestCase):

diff --git a/tests/utils/tile_utils_tests.py b/tests/utils/tile_utils_tests.py
@@ -7,8 +7,8 @@
 from testfixtures import TempDirectory
 import unittest
 
-import micro_dl.utils.tile_utils as tile_utils
-import micro_dl.utils.aux_utils as aux_utils
+import viscy.utils.tile_utils as tile_utils
+import viscy.utils.aux_utils as aux_utils
 
 
 class TestTileUtils(unittest.TestCase):

diff --git a/micro_dl/__init__.py → viscy/__init__.py b/micro_dl/__init__.py → viscy/__init__.py
diff --git a/micro_dl/cli/__init__.py → viscy/cli/__init__.py b/micro_dl/cli/__init__.py → viscy/cli/__init__.py
diff --git a/micro_dl/cli/cli.py → viscy/cli/cli.py b/micro_dl/cli/cli.py → viscy/cli/cli.py
@@ -4,8 +4,8 @@
 from jsonargparse import lazy_instance
 from lightning.pytorch.cli import LightningCLI
 from lightning.pytorch.loggers import TensorBoardLogger
-from micro_dl.light.data import HCSDataModule
-from micro_dl.light.engine import PhaseToNuc25D
+from viscy.light.data import HCSDataModule
+from viscy.light.engine import PhaseToNuc25D
 
 
 class VSLightningCLI(LightningCLI):

diff --git a/micro_dl/cli/curator_script.py → viscy/cli/curator_script.py b/micro_dl/cli/curator_script.py → viscy/cli/curator_script.py
@@ -9,8 +9,8 @@
 import iohub.ngff as ngff
 import argparse
 
-import micro_dl.evaluation.evaluation_metrics as metrics
-import micro_dl.utils.aux_utils as aux_utils
+import viscy.evaluation.evaluation_metrics as metrics
+import viscy.utils.aux_utils as aux_utils
 # from waveorder.focus import focus_from_transverse_band
 
 # %% read the below details from the config file

diff --git a/micro_dl/cli/fit_example.yml → viscy/cli/fit_example.yml b/micro_dl/cli/fit_example.yml → viscy/cli/fit_example.yml
diff --git a/micro_dl/cli/metrics_script.py → viscy/cli/metrics_script.py b/micro_dl/cli/metrics_script.py → viscy/cli/metrics_script.py
@@ -8,8 +8,8 @@
 import argparse
 import pandas as pd
 
-import micro_dl.evaluation.evaluation_metrics as metrics
-import micro_dl.utils.aux_utils as aux_utils
+import viscy.evaluation.evaluation_metrics as metrics
+import viscy.utils.aux_utils as aux_utils
 
 # %% read the below details from the config file
 

diff --git a/micro_dl/cli/onnx_export_script.py → viscy/cli/onnx_export_script.py b/micro_dl/cli/onnx_export_script.py → viscy/cli/onnx_export_script.py
@@ -9,7 +9,7 @@
 import torch
 
 sys.path.insert(0, "/home/christian.foley/virtual_staining/workspaces/microDL")
-import micro_dl.inference.inference as inference
+import viscy.inference.inference as inference
 
 def parse_args():
     """

diff --git a/micro_dl/cli/predict_example.yml → viscy/cli/predict_example.yml b/micro_dl/cli/predict_example.yml → viscy/cli/predict_example.yml