From 49930ac1d294c04a2c54328c0c274fbb9639c4f6 Mon Sep 17 00:00:00 2001 From: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> Date: Tue, 30 May 2023 10:36:07 -0700 Subject: [PATCH] rename the micro_dl module to viscy --- scripts/test_zarr_reading.py | 4 ++-- scripts/visualize_data_augmentation.py | 4 ++-- tests/cli/inference_script_tests.py | 4 ++-- tests/cli/metrics_script_tests.py | 6 +++--- tests/cli/preprocess_script_test.py | 6 +++--- tests/evaluation/evaluation_metrics_tests.py | 2 +- tests/input/dataset_tests.py | 2 +- tests/input/dataset_with_mask_tests.py | 2 +- tests/input/inference_dataset_tests.py | 4 ++-- tests/networks/conv_blocks_tests.py | 6 +++--- tests/networks/image2D_to_vector_net_tests.py | 2 +- tests/networks/image3D_to_vector_net_tests.py | 2 +- tests/networks/unet2D_tests.py | 2 +- tests/networks/unet3D_tests.py | 2 +- tests/networks/unet_stack_2D_tests.py | 2 +- tests/networks/unet_stack_to_stack_tests.py | 2 +- tests/plotting/plot_utils_tests.py | 2 +- tests/preprocessing/generate_masks_tests.py | 4 ++-- tests/preprocessing/resize_images_tests.py | 4 ++-- tests/torch_unet/networks/Unet25D_tests.py | 4 ++-- tests/torch_unet/networks/Unet2D_tests.py | 4 ++-- tests/torch_unet/networks/layers/ConvBlock2D_tests.py | 4 ++-- tests/torch_unet/networks/layers/ConvBlock3D_tests.py | 4 ++-- tests/torch_unet/utils/dataset_tests.py | 6 +++--- tests/torch_unet/utils/training_tests.py | 4 ++-- tests/utils/aux_utils_tests.py | 2 +- tests/utils/image_utils_tests.py | 8 ++++---- tests/utils/io_utils_tests.py | 2 +- tests/utils/masks_utils_tests.py | 2 +- tests/utils/meta_utils_tests.py | 4 ++-- tests/utils/mp_utils_tests.py | 8 ++++---- tests/utils/preprocess_utils_tests.py | 4 ++-- tests/utils/tile_utils_tests.py | 4 ++-- {micro_dl => viscy}/__init__.py | 0 {micro_dl => viscy}/cli/__init__.py | 0 {micro_dl => viscy}/cli/cli.py | 4 ++-- {micro_dl => viscy}/cli/curator_script.py | 4 ++-- {micro_dl => viscy}/cli/fit_example.yml | 0 {micro_dl => viscy}/cli/metrics_script.py | 4 ++-- {micro_dl => viscy}/cli/onnx_export_script.py | 2 +- {micro_dl => viscy}/cli/predict_example.yml | 0 {micro_dl => viscy}/cli/preprocess_script.py | 6 +++--- {micro_dl => viscy}/cli/readme.md | 0 {micro_dl => viscy}/data_organization.md | 0 {micro_dl => viscy}/evaluation/evaluation.py | 2 +- {micro_dl => viscy}/evaluation/evaluation_metrics.py | 0 {micro_dl => viscy}/light/data.py | 0 {micro_dl => viscy}/light/engine.py | 4 ++-- {micro_dl => viscy}/light/prediction_writer.py | 2 +- {micro_dl => viscy}/plotting/__init__.py | 0 {micro_dl => viscy}/plotting/plot_utils.py | 2 +- {micro_dl => viscy}/preprocessing/generate_masks.py | 4 ++-- {micro_dl => viscy}/preprocessing/preprocessing.md | 0 {micro_dl => viscy}/preprocessing/readme.md | 0 {micro_dl => viscy}/readme.md | 0 {micro_dl => viscy}/scripts/README.md | 0 {micro_dl => viscy}/scripts/export_from_tensorboard.py | 0 {micro_dl => viscy}/scripts/gpu_usage_monitor.py | 2 +- {micro_dl => viscy}/scripts/log_feature_map.py | 2 +- {micro_dl => viscy}/scripts/profiling.py | 2 +- {micro_dl => viscy}/torch_unet/networks/Unet25D.py | 4 ++-- {micro_dl => viscy}/torch_unet/networks/Unet2D.py | 2 +- .../torch_unet/networks/layers/ConvBlock2D.py | 0 .../torch_unet/networks/layers/ConvBlock3D.py | 0 {micro_dl => viscy}/torch_unet/utils/logging.py | 4 ++-- {micro_dl => viscy}/torch_unet/utils/model.py | 4 ++-- {micro_dl => viscy}/utils/__init__.py | 0 {micro_dl => viscy}/utils/aux_utils.py | 0 {micro_dl => viscy}/utils/cli_utils.py | 0 {micro_dl => viscy}/utils/image_utils.py | 4 ++-- {micro_dl => viscy}/utils/masks.py | 2 +- {micro_dl => viscy}/utils/meta_utils.py | 4 ++-- {micro_dl => viscy}/utils/mp_utils.py | 4 ++-- {micro_dl => viscy}/utils/network_utils.py | 0 {micro_dl => viscy}/utils/normalize.py | 0 {micro_dl => viscy}/utils/preprocess_utils.py | 2 +- {micro_dl => viscy}/utils/tile_utils.py | 2 +- 77 files changed, 97 insertions(+), 97 deletions(-) rename {micro_dl => viscy}/__init__.py (100%) rename {micro_dl => viscy}/cli/__init__.py (100%) rename {micro_dl => viscy}/cli/cli.py (95%) rename {micro_dl => viscy}/cli/curator_script.py (98%) rename {micro_dl => viscy}/cli/fit_example.yml (100%) rename {micro_dl => viscy}/cli/metrics_script.py (97%) rename {micro_dl => viscy}/cli/onnx_export_script.py (99%) rename {micro_dl => viscy}/cli/predict_example.yml (100%) rename {micro_dl => viscy}/cli/preprocess_script.py (96%) rename {micro_dl => viscy}/cli/readme.md (100%) rename {micro_dl => viscy}/data_organization.md (100%) rename {micro_dl => viscy}/evaluation/evaluation.py (99%) rename {micro_dl => viscy}/evaluation/evaluation_metrics.py (100%) rename {micro_dl => viscy}/light/data.py (100%) rename {micro_dl => viscy}/light/engine.py (97%) rename {micro_dl => viscy}/light/prediction_writer.py (99%) rename {micro_dl => viscy}/plotting/__init__.py (100%) rename {micro_dl => viscy}/plotting/plot_utils.py (99%) rename {micro_dl => viscy}/preprocessing/generate_masks.py (97%) rename {micro_dl => viscy}/preprocessing/preprocessing.md (100%) rename {micro_dl => viscy}/preprocessing/readme.md (100%) rename {micro_dl => viscy}/readme.md (100%) rename {micro_dl => viscy}/scripts/README.md (100%) rename {micro_dl => viscy}/scripts/export_from_tensorboard.py (100%) rename {micro_dl => viscy}/scripts/gpu_usage_monitor.py (98%) rename {micro_dl => viscy}/scripts/log_feature_map.py (93%) rename {micro_dl => viscy}/scripts/profiling.py (94%) rename {micro_dl => viscy}/torch_unet/networks/Unet25D.py (98%) rename {micro_dl => viscy}/torch_unet/networks/Unet2D.py (99%) rename {micro_dl => viscy}/torch_unet/networks/layers/ConvBlock2D.py (100%) rename {micro_dl => viscy}/torch_unet/networks/layers/ConvBlock3D.py (100%) rename {micro_dl => viscy}/torch_unet/utils/logging.py (99%) rename {micro_dl => viscy}/torch_unet/utils/model.py (97%) rename {micro_dl => viscy}/utils/__init__.py (100%) rename {micro_dl => viscy}/utils/aux_utils.py (100%) rename {micro_dl => viscy}/utils/cli_utils.py (100%) rename {micro_dl => viscy}/utils/image_utils.py (99%) rename {micro_dl => viscy}/utils/masks.py (99%) rename {micro_dl => viscy}/utils/meta_utils.py (98%) rename {micro_dl => viscy}/utils/mp_utils.py (99%) rename {micro_dl => viscy}/utils/network_utils.py (100%) rename {micro_dl => viscy}/utils/normalize.py (100%) rename {micro_dl => viscy}/utils/preprocess_utils.py (99%) rename {micro_dl => viscy}/utils/tile_utils.py (99%) diff --git a/scripts/test_zarr_reading.py b/scripts/test_zarr_reading.py index 795424b71..584286f61 100644 --- 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 index ddd714cb5..dfae353a9 100644 --- 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 index 4fa13b1f0..449174f77 100644 --- 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 index 38a5e8cce..3498c8e1f 100644 --- 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 index ed59ddeaa..f60303239 100644 --- 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 index 778477ee8..de0f4f600 100644 --- 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 index 659772108..330e1b44c 100644 --- 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 index 9b660cc42..5b46272bd 100644 --- 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 index 67c3b0a44..31b60f6e4 100644 --- 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 index b91ab698e..a157b44c7 100644 --- 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 index f0a2ef81c..110b37c3a 100644 --- 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 index 4c680e5c9..baa8b8071 100644 --- 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 index 7fbac8a22..cf92509dc 100644 --- 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 index b55264f6e..993aca68c 100644 --- 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 index b61635522..3aab1334b 100644 --- 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 index 8a018b8aa..8ee20be33 100644 --- 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 index 4d0fc5e66..887a86786 100644 --- 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 index 03461461e..6f40c3bb1 100644 --- 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 index d2f18f88c..1232ff990 100644 --- 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 index 70877591d..c2e37b1bc 100644 --- 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 index bca275a22..ed7230048 100644 --- 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 index c30cfa6f3..6aef09b30 100644 --- 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 index e6a856ac1..160f4914f 100644 --- 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 index 60d14184b..7c7c5f16e 100644 --- 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 index 1f7f21df5..5209a804d 100644 --- 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 index 600694721..c12832cd5 100644 --- 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 index e806e7330..dadf882b4 100644 --- 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 index b7915cc7a..c6809235d 100644 --- 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 index 4692ef932..498e0bee5 100644 --- 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 index 013a04335..29e34ba9b 100644 --- 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 index 940e3fafe..880cdd948 100644 --- 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 index a64a41e4c..a31caf9fc 100644 --- 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 index 583dc480e..b4e2e5a43 100644 --- 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 b/viscy/__init__.py similarity index 100% rename from micro_dl/__init__.py rename to viscy/__init__.py diff --git a/micro_dl/cli/__init__.py b/viscy/cli/__init__.py similarity index 100% rename from micro_dl/cli/__init__.py rename to viscy/cli/__init__.py diff --git a/micro_dl/cli/cli.py b/viscy/cli/cli.py similarity index 95% rename from micro_dl/cli/cli.py rename to viscy/cli/cli.py index 86321689f..1f1f2791c 100644 --- a/micro_dl/cli/cli.py +++ b/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 b/viscy/cli/curator_script.py similarity index 98% rename from micro_dl/cli/curator_script.py rename to viscy/cli/curator_script.py index 8cb90e735..60c1fed86 100644 --- a/micro_dl/cli/curator_script.py +++ b/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 b/viscy/cli/fit_example.yml similarity index 100% rename from micro_dl/cli/fit_example.yml rename to viscy/cli/fit_example.yml diff --git a/micro_dl/cli/metrics_script.py b/viscy/cli/metrics_script.py similarity index 97% rename from micro_dl/cli/metrics_script.py rename to viscy/cli/metrics_script.py index ac2e9ae0d..1b59aec44 100644 --- a/micro_dl/cli/metrics_script.py +++ b/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 b/viscy/cli/onnx_export_script.py similarity index 99% rename from micro_dl/cli/onnx_export_script.py rename to viscy/cli/onnx_export_script.py index edf12c93d..4c07c3bcd 100644 --- a/micro_dl/cli/onnx_export_script.py +++ b/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 b/viscy/cli/predict_example.yml similarity index 100% rename from micro_dl/cli/predict_example.yml rename to viscy/cli/predict_example.yml diff --git a/micro_dl/cli/preprocess_script.py b/viscy/cli/preprocess_script.py similarity index 96% rename from micro_dl/cli/preprocess_script.py rename to viscy/cli/preprocess_script.py index 4af5790ae..cfc66197e 100644 --- a/micro_dl/cli/preprocess_script.py +++ b/viscy/cli/preprocess_script.py @@ -3,9 +3,9 @@ import iohub.ngff as ngff import time -from micro_dl.preprocessing.generate_masks import MaskProcessor -import micro_dl.utils.aux_utils as aux_utils -import micro_dl.utils.meta_utils as meta_utils +from viscy.preprocessing.generate_masks import MaskProcessor +import viscy.utils.aux_utils as aux_utils +import viscy.utils.meta_utils as meta_utils def parse_args(): diff --git a/micro_dl/cli/readme.md b/viscy/cli/readme.md similarity index 100% rename from micro_dl/cli/readme.md rename to viscy/cli/readme.md diff --git a/micro_dl/data_organization.md b/viscy/data_organization.md similarity index 100% rename from micro_dl/data_organization.md rename to viscy/data_organization.md diff --git a/micro_dl/evaluation/evaluation.py b/viscy/evaluation/evaluation.py similarity index 99% rename from micro_dl/evaluation/evaluation.py rename to viscy/evaluation/evaluation.py index 77f19cddf..c81a61de1 100644 --- a/micro_dl/evaluation/evaluation.py +++ b/viscy/evaluation/evaluation.py @@ -1,5 +1,5 @@ import numpy as np -import micro_dl.evaluation.evaluation_metrics as inference_metrics +import viscy.evaluation.evaluation_metrics as inference_metrics from torch.utils.tensorboard import SummaryWriter diff --git a/micro_dl/evaluation/evaluation_metrics.py b/viscy/evaluation/evaluation_metrics.py similarity index 100% rename from micro_dl/evaluation/evaluation_metrics.py rename to viscy/evaluation/evaluation_metrics.py diff --git a/micro_dl/light/data.py b/viscy/light/data.py similarity index 100% rename from micro_dl/light/data.py rename to viscy/light/data.py diff --git a/micro_dl/light/engine.py b/viscy/light/engine.py similarity index 97% rename from micro_dl/light/engine.py rename to viscy/light/engine.py index 9f7b6f49c..bc978bf93 100644 --- a/micro_dl/light/engine.py +++ b/viscy/light/engine.py @@ -11,8 +11,8 @@ from skimage.exposure import rescale_intensity from torch.optim.lr_scheduler import ConstantLR -from micro_dl.torch_unet.networks.Unet25D import Unet25d -from micro_dl.torch_unet.utils.model import ModelDefaults25D, define_model +from viscy.torch_unet.networks.Unet25D import Unet25d +from viscy.torch_unet.utils.model import ModelDefaults25D, define_model class PhaseToNuc25D(LightningModule): diff --git a/micro_dl/light/prediction_writer.py b/viscy/light/prediction_writer.py similarity index 99% rename from micro_dl/light/prediction_writer.py rename to viscy/light/prediction_writer.py index de5b3f376..40c7bf565 100644 --- a/micro_dl/light/prediction_writer.py +++ b/viscy/light/prediction_writer.py @@ -7,7 +7,7 @@ from lightning.pytorch.callbacks import BasePredictionWriter import torch -from micro_dl.light.data import Sample +from viscy.light.data import Sample class HCSPredictionWriter(BasePredictionWriter): diff --git a/micro_dl/plotting/__init__.py b/viscy/plotting/__init__.py similarity index 100% rename from micro_dl/plotting/__init__.py rename to viscy/plotting/__init__.py diff --git a/micro_dl/plotting/plot_utils.py b/viscy/plotting/plot_utils.py similarity index 99% rename from micro_dl/plotting/plot_utils.py rename to viscy/plotting/plot_utils.py index bd1b3a830..bb2f6b952 100644 --- a/micro_dl/plotting/plot_utils.py +++ b/viscy/plotting/plot_utils.py @@ -9,7 +9,7 @@ import numpy as np import os import sys -from micro_dl.utils.normalize import hist_clipping +from viscy.utils.normalize import hist_clipping from mpl_toolkits.axes_grid1 import make_axes_locatable diff --git a/micro_dl/preprocessing/generate_masks.py b/viscy/preprocessing/generate_masks.py similarity index 97% rename from micro_dl/preprocessing/generate_masks.py rename to viscy/preprocessing/generate_masks.py index 89a4a286b..f2ffde989 100644 --- a/micro_dl/preprocessing/generate_masks.py +++ b/viscy/preprocessing/generate_masks.py @@ -3,8 +3,8 @@ import os import pandas as pd -import micro_dl.utils.aux_utils as aux_utils -from micro_dl.utils.mp_utils import mp_create_and_write_mask +import viscy.utils.aux_utils as aux_utils +from viscy.utils.mp_utils import mp_create_and_write_mask class MaskProcessor: diff --git a/micro_dl/preprocessing/preprocessing.md b/viscy/preprocessing/preprocessing.md similarity index 100% rename from micro_dl/preprocessing/preprocessing.md rename to viscy/preprocessing/preprocessing.md diff --git a/micro_dl/preprocessing/readme.md b/viscy/preprocessing/readme.md similarity index 100% rename from micro_dl/preprocessing/readme.md rename to viscy/preprocessing/readme.md diff --git a/micro_dl/readme.md b/viscy/readme.md similarity index 100% rename from micro_dl/readme.md rename to viscy/readme.md diff --git a/micro_dl/scripts/README.md b/viscy/scripts/README.md similarity index 100% rename from micro_dl/scripts/README.md rename to viscy/scripts/README.md diff --git a/micro_dl/scripts/export_from_tensorboard.py b/viscy/scripts/export_from_tensorboard.py similarity index 100% rename from micro_dl/scripts/export_from_tensorboard.py rename to viscy/scripts/export_from_tensorboard.py diff --git a/micro_dl/scripts/gpu_usage_monitor.py b/viscy/scripts/gpu_usage_monitor.py similarity index 98% rename from micro_dl/scripts/gpu_usage_monitor.py rename to viscy/scripts/gpu_usage_monitor.py index 1ab4831a5..c873a4b15 100644 --- a/micro_dl/scripts/gpu_usage_monitor.py +++ b/viscy/scripts/gpu_usage_monitor.py @@ -117,7 +117,7 @@ def main(): start = time.time() if args.mode != "listen": - import micro_dl.cli.torch_train_script as training + import viscy.cli.torch_train_script as training p = multiprocessing.Process( target=training.main, diff --git a/micro_dl/scripts/log_feature_map.py b/viscy/scripts/log_feature_map.py similarity index 93% rename from micro_dl/scripts/log_feature_map.py rename to viscy/scripts/log_feature_map.py index 142de209b..17a9c3012 100644 --- a/micro_dl/scripts/log_feature_map.py +++ b/viscy/scripts/log_feature_map.py @@ -5,7 +5,7 @@ import sys sys.path.insert(0, "/home/christian.foley/virtual_staining/microDL") -import micro_dl.utils.cli_utils as cli_utils +import viscy.utils.cli_utils as cli_utils def main(): diff --git a/micro_dl/scripts/profiling.py b/viscy/scripts/profiling.py similarity index 94% rename from micro_dl/scripts/profiling.py rename to viscy/scripts/profiling.py index 490db0f94..8017232a5 100644 --- a/micro_dl/scripts/profiling.py +++ b/viscy/scripts/profiling.py @@ -1,6 +1,6 @@ # script to profile dataloading -from micro_dl.light.data import HCSDataModule +from viscy.light.data import HCSDataModule from numcodecs import blosc from profilehooks import profile diff --git a/micro_dl/torch_unet/networks/Unet25D.py b/viscy/torch_unet/networks/Unet25D.py similarity index 98% rename from micro_dl/torch_unet/networks/Unet25D.py rename to viscy/torch_unet/networks/Unet25D.py index d65af49c1..20c6e6ee7 100644 --- a/micro_dl/torch_unet/networks/Unet25D.py +++ b/viscy/torch_unet/networks/Unet25D.py @@ -5,8 +5,8 @@ import torch import torch.nn as nn -from micro_dl.torch_unet.networks.layers.ConvBlock3D import * -import micro_dl.torch_unet.utils.logging as log +from viscy.torch_unet.networks.layers.ConvBlock3D import * +import viscy.torch_unet.utils.logging as log class Unet25d(nn.Module): diff --git a/micro_dl/torch_unet/networks/Unet2D.py b/viscy/torch_unet/networks/Unet2D.py similarity index 99% rename from micro_dl/torch_unet/networks/Unet2D.py rename to viscy/torch_unet/networks/Unet2D.py index 2bd2ac4b0..ae915d208 100644 --- a/micro_dl/torch_unet/networks/Unet2D.py +++ b/viscy/torch_unet/networks/Unet2D.py @@ -1,7 +1,7 @@ import torch import torch.nn as nn -from micro_dl.torch_unet.networks.layers.ConvBlock2D import * +from viscy.torch_unet.networks.layers.ConvBlock2D import * class Unet2d(nn.Module): diff --git a/micro_dl/torch_unet/networks/layers/ConvBlock2D.py b/viscy/torch_unet/networks/layers/ConvBlock2D.py similarity index 100% rename from micro_dl/torch_unet/networks/layers/ConvBlock2D.py rename to viscy/torch_unet/networks/layers/ConvBlock2D.py diff --git a/micro_dl/torch_unet/networks/layers/ConvBlock3D.py b/viscy/torch_unet/networks/layers/ConvBlock3D.py similarity index 100% rename from micro_dl/torch_unet/networks/layers/ConvBlock3D.py rename to viscy/torch_unet/networks/layers/ConvBlock3D.py diff --git a/micro_dl/torch_unet/utils/logging.py b/viscy/torch_unet/utils/logging.py similarity index 99% rename from micro_dl/torch_unet/utils/logging.py rename to viscy/torch_unet/utils/logging.py index 59b3fb646..0b045dacb 100644 --- a/micro_dl/torch_unet/utils/logging.py +++ b/viscy/torch_unet/utils/logging.py @@ -6,8 +6,8 @@ import torch -from micro_dl.utils.cli_utils import save_figure -from micro_dl.utils.normalize import hist_clipping +from viscy.utils.cli_utils import save_figure +from viscy.utils.normalize import hist_clipping def log_feature(feature_map, name, log_save_folder, debug_mode): diff --git a/micro_dl/torch_unet/utils/model.py b/viscy/torch_unet/utils/model.py similarity index 97% rename from micro_dl/torch_unet/utils/model.py rename to viscy/torch_unet/utils/model.py index cd1ede9c5..cad36c0f1 100644 --- a/micro_dl/torch_unet/utils/model.py +++ b/viscy/torch_unet/utils/model.py @@ -1,5 +1,5 @@ -import micro_dl.torch_unet.networks.Unet25D as Unet25D -import micro_dl.torch_unet.networks.Unet2D as Unet2D +import viscy.torch_unet.networks.Unet25D as Unet25D +import viscy.torch_unet.networks.Unet2D as Unet2D import os import torch import matplotlib.pyplot as plt diff --git a/micro_dl/utils/__init__.py b/viscy/utils/__init__.py similarity index 100% rename from micro_dl/utils/__init__.py rename to viscy/utils/__init__.py diff --git a/micro_dl/utils/aux_utils.py b/viscy/utils/aux_utils.py similarity index 100% rename from micro_dl/utils/aux_utils.py rename to viscy/utils/aux_utils.py diff --git a/micro_dl/utils/cli_utils.py b/viscy/utils/cli_utils.py similarity index 100% rename from micro_dl/utils/cli_utils.py rename to viscy/utils/cli_utils.py diff --git a/micro_dl/utils/image_utils.py b/viscy/utils/image_utils.py similarity index 99% rename from micro_dl/utils/image_utils.py rename to viscy/utils/image_utils.py index 258d1d44f..47d500514 100644 --- a/micro_dl/utils/image_utils.py +++ b/viscy/utils/image_utils.py @@ -11,8 +11,8 @@ from skimage.transform import resize import iohub.ngff as ngff -import micro_dl.utils.aux_utils as aux_utils -import micro_dl.utils.normalize as normalize +import viscy.utils.aux_utils as aux_utils +import viscy.utils.normalize as normalize def im_bit_convert(im, bit=16, norm=False, limit=[]): diff --git a/micro_dl/utils/masks.py b/viscy/utils/masks.py similarity index 99% rename from micro_dl/utils/masks.py rename to viscy/utils/masks.py index 82d02d8bd..cd46faed3 100644 --- a/micro_dl/utils/masks.py +++ b/viscy/utils/masks.py @@ -9,7 +9,7 @@ remove_small_objects, binary_dilation, ) -from micro_dl.utils.image_utils import im_adjust +from viscy.utils.image_utils import im_adjust def create_otsu_mask(input_image, sigma=0.6): diff --git a/micro_dl/utils/meta_utils.py b/viscy/utils/meta_utils.py similarity index 98% rename from micro_dl/utils/meta_utils.py rename to viscy/utils/meta_utils.py index a364a11a8..e0a522dd3 100644 --- a/micro_dl/utils/meta_utils.py +++ b/viscy/utils/meta_utils.py @@ -4,8 +4,8 @@ import pandas as pd import sys -import micro_dl.utils.mp_utils as mp_utils -from micro_dl.utils.cli_utils import show_progress_bar +import viscy.utils.mp_utils as mp_utils +from viscy.utils.cli_utils import show_progress_bar def write_meta_field(position: ngff.Position, metadata, field_name, subfield_name): diff --git a/micro_dl/utils/mp_utils.py b/viscy/utils/mp_utils.py similarity index 99% rename from micro_dl/utils/mp_utils.py rename to viscy/utils/mp_utils.py index cd1e4a62b..550b4f210 100644 --- a/micro_dl/utils/mp_utils.py +++ b/viscy/utils/mp_utils.py @@ -3,8 +3,8 @@ import numpy as np import scipy.stats -import micro_dl.utils.image_utils as image_utils -import micro_dl.utils.masks as mask_utils +import viscy.utils.image_utils as image_utils +import viscy.utils.masks as mask_utils def mp_wrapper(fn, fn_args, workers): diff --git a/micro_dl/utils/network_utils.py b/viscy/utils/network_utils.py similarity index 100% rename from micro_dl/utils/network_utils.py rename to viscy/utils/network_utils.py diff --git a/micro_dl/utils/normalize.py b/viscy/utils/normalize.py similarity index 100% rename from micro_dl/utils/normalize.py rename to viscy/utils/normalize.py diff --git a/micro_dl/utils/preprocess_utils.py b/viscy/utils/preprocess_utils.py similarity index 99% rename from micro_dl/utils/preprocess_utils.py rename to viscy/utils/preprocess_utils.py index 4cfecaef2..3e019be15 100644 --- a/micro_dl/utils/preprocess_utils.py +++ b/viscy/utils/preprocess_utils.py @@ -3,7 +3,7 @@ import os import pandas as pd -import micro_dl.utils.aux_utils as aux_utils +import viscy.utils.aux_utils as aux_utils def get_preprocess_config(data_dir): diff --git a/micro_dl/utils/tile_utils.py b/viscy/utils/tile_utils.py similarity index 99% rename from micro_dl/utils/tile_utils.py rename to viscy/utils/tile_utils.py index e24c33a2a..4ab0d1cc6 100644 --- a/micro_dl/utils/tile_utils.py +++ b/viscy/utils/tile_utils.py @@ -3,7 +3,7 @@ import numpy as np import pandas as pd -import micro_dl.utils.aux_utils as aux_utils +import viscy.utils.aux_utils as aux_utils def tile_image(input_image,