From 735ab59cc1b3ca6e5c0a24f84268622f764fb636 Mon Sep 17 00:00:00 2001 From: mariana-gferreira Date: Fri, 18 Oct 2024 17:37:12 +0100 Subject: [PATCH] core-0.6.10, bug fixes --- Colab_notebooks/Latest_Notebook_versions.csv | 2 +- .../U-Net_2D_Multilabel_ZeroCostDL4Mic.ipynb | 172 +++++++----------- 2 files changed, 70 insertions(+), 104 deletions(-) diff --git a/Colab_notebooks/Latest_Notebook_versions.csv b/Colab_notebooks/Latest_Notebook_versions.csv index 22b09ea..001f686 100644 --- a/Colab_notebooks/Latest_Notebook_versions.csv +++ b/Colab_notebooks/Latest_Notebook_versions.csv @@ -14,7 +14,7 @@ fnet (2D),1.14.1 fnet (3D),1.13.1 U-Net (2D),2.2.1 U-Net (3D),2.2.1 -U-Net (2D) multilabel,2.1.3 +U-Net (2D) multilabel,2.1.4 Kaibu,1.13.2 MaskRCNN,1.14.1 Noise2Void (2D),1.16.2 diff --git a/Colab_notebooks/U-Net_2D_Multilabel_ZeroCostDL4Mic.ipynb b/Colab_notebooks/U-Net_2D_Multilabel_ZeroCostDL4Mic.ipynb index f9abcd9..4aab199 100644 --- a/Colab_notebooks/U-Net_2D_Multilabel_ZeroCostDL4Mic.ipynb +++ b/Colab_notebooks/U-Net_2D_Multilabel_ZeroCostDL4Mic.ipynb @@ -207,7 +207,7 @@ "outputs": [], "source": [ "from __future__ import print_function\n", - "Notebook_version = '2.1.3'\n", + "Notebook_version = '2.1.4'\n", "Network = 'U-Net (2D) multilabel'\n", "\n", "from builtins import any as b_any\n", @@ -324,6 +324,7 @@ "from bioimageio.spec import save_bioimageio_package\n", "from bioimageio.spec._internal.io import FileDescr\n", "import bioimageio.core as bioimageio_core\n", + "from bioimageio.core.weight_converter.keras._tensorflow import convert_weights_to_tensorflow_saved_model_bundle\n", "from zipfile import ZipFile\n", "import requests\n", "from bioimageio.spec.pretty_validation_errors import (\n", @@ -790,56 +791,6 @@ " mask[mask <= threshold] = 0\n", " return mask\n", "\n", - "# BMZ model export functions\n", - "def make_author(author_input_info: str):\n", - " \"\"\"\n", - " Create an Author object from a string input.\n", - "\n", - " Args:\n", - " author_input_info: A string containing the author's name and affiliation.\n", - "\n", - " Returns:\n", - " An Author object\n", - " \"\"\"\n", - " if author_input_info.strip() == '':\n", - " return None\n", - "\n", - " auth_order = ['name', 'affiliation', 'email', 'orcid', 'github_user']\n", - " auth_dict = {}\n", - "\n", - " auth_info_split = author_input_info.split(',')\n", - "\n", - " for i in range(len(auth_info_split)):\n", - " if auth_info_split[i].strip() == 'None' or auth_info_split[i].strip() == '':\n", - " continue\n", - " else:\n", - " auth_dict[auth_order[i]] = auth_info_split[i].strip()\n", - "\n", - " return bioimageio_spec.Author(**auth_dict)\n", - "\n", - "def make_maintainer(maintainer_input_info: str):\n", - " \"\"\"\n", - " Create an Author object from a string input.\n", - "\n", - " Args:\n", - " author_input_info: A string containing the author's name and affiliation.\n", - "\n", - " Returns:\n", - " An Author object\n", - " \"\"\"\n", - " maint_order = [ 'github_user', 'name', 'affiliation', 'email', 'orcid']\n", - " maint_dict = {}\n", - "\n", - " maint_info_split = maintainer_input_info.split(',')\n", - "\n", - " for i in range(len(maint_info_split)):\n", - " if maint_info_split[i].strip() == 'None' or maint_info_split[i].strip() == '':\n", - " continue\n", - " else:\n", - " maint_dict[maint_order[i]] = maint_info_split[i].strip()\n", - "\n", - " return bioimageio_spec.Maintainer(**maint_dict)\n", - "\n", "\n", "# -------------- Other definitions -----------\n", "W = '\\033[0m' # white (normal)\n", @@ -1331,7 +1282,7 @@ "outputs": [], "source": [ "# ------------- Initial user input ------------\n", - "#@markdown ###Path to training images:\n", + "#@markdown ### Path to training images:\n", "Training_source = '' #@param {type:\"string\"}\n", "Training_target = '' #@param {type:\"string\"}\n", "\n", @@ -1339,15 +1290,17 @@ "model_path = '' #@param {type:\"string\"}\n", "\n", "labels = 3 #@param {type:\"number\"}\n", + "# @markdown\n", "\n", - "#@markdown ###Training parameters:\n", + "#@markdown ### Training parameters:\n", "#@markdown Number of epochs\n", "number_of_epochs = 10#@param {type:\"number\"}\n", + "# @markdown\n", "\n", - "#@markdown ###Advanced parameters:\n", + "#@markdown ### Advanced parameters:\n", "Use_Default_Advanced_Parameters = True #@param {type:\"boolean\"}\n", "\n", - "#@markdown ###If not, please input:\n", + "#@markdown ### If not, please input:\n", "batch_size = 5#@param {type:\"integer\"}\n", "number_of_steps = 0#@param {type:\"number\"}\n", "pooling_steps = 3 #@param [1,2,3,4]{type:\"raw\"}\n", @@ -2176,53 +2129,62 @@ "source": [ "# ------------- User input ------------\n", "# information about the model\n", - "#@markdown ##Insert the information to document your model:\n", + "#@markdown ### Insert the information to document your model:\n", "Trained_model_name = \"\" #@param {type:\"string\"}\n", "Trained_model_description = \"\" #@param {type:\"string\"}\n", + "# @markdown \n", + "\n", + "#@markdown ### Author(s) names, comma separated:\n", + "author_name = \"Author 1 name, Author 2 name, Author 3 name\" #@param {type:\"string\"}\n", "\n", - "#@markdown ###Author(s) - insert information separated by commas:\n", - "Trained_model_author_1 = \"Author 1 name, *Author 1 affiliation, *Author 1 email, *Author 1 ORCID, *Author 1 Github User\" #@param {type:\"string\"}\n", - "Trained_model_author_2 = \"Author 2 name, *Author 2 affiliation, *Author 2 email, *Author 2 ORCID, *Author 2 Github User\" #@param {type:\"string\"}\n", + "# @markdown\n", "\n", - "# @markdown ###Model Packager:\n", - "packager_same_as_author = True #@param {type:\"boolean\"}\n", - "#@markdown - If not, please, provide the following information:\n", - "Trained_model_packager = \"Packager name, *Packager affiliation, *Packager email, *Packager ORCID, *Packager Github User\" #@param {type:\"string\"}\n", + "# @markdown ### Model Packager position in the list of authors:\n", + "# @markdown E.g.: 1 for Author 1, 2 for Author 2, etc.\n", + "Trained_model_packager = 1 #@param {type:\"number\"}\n", + "# @markdown\n", "\n", - "# @markdown ###Model Maintainer:\n", - "maintainer_same_as_author = True #@param {type:\"boolean\"}\n", - "#@markdown - If not, please, provide the following information:\n", - "Trained_model_maintainer = \"Maintainer Github User, *Maintainer name, *Maintainer affiliation, *Maintainer email, *Maintainer ORCID\" #@param {type:\"string\"}\n", + "# @markdown ### Model Maintainer:\n", + "Trained_model_maintainer = \"Maintainer Github User\" #@param {type:\"string\"}\n", + "# @markdown #### If maintainer name is in author list provide the corresponding number:\n", + "# @markdown E.g.: 1 for Author 1, 2 for Author 2, etc.\n", + "maintainer_author_number = 1 #@param {type:\"number\"}\n", "\n", - "# @markdown ###License:\n", - "Trained_model_license = 'CC-BY-4.0' #@param {type:\"string\"}\n", + "# @markdown\n", "\n", + "# @markdown ### License:\n", + "Trained_model_license = 'CC-BY-4.0' #@param [\"BSD-Protection\", \"CC-BY-SA-2.0\", \"Unicode-DFS-2016\", \"CC-BY-ND-2.5\", \"CC-BY-NC-ND-3.0\", \"BSD-3-Clause-LBNL\", \"NCGL-UK-2.0\", \"GPL-1.0+\", \"OSL-1.0\", \"MIT\", \"MPL-2.0\", \"CC-BY-NC-1.0\", \"CC-BY-NC-ND-2.5\", \"CC-BY-SA-2.0-UK\", \"BSD-4-Clause-Shortened\", \"CC-BY-4.0\"]\n", "Trained_model_references = [\"Falk et al. Nature Methods 2019\", \"Ronneberger et al. arXiv in 2015\", \"Lucas von Chamier et al. biorXiv 2020\"]\n", "Trained_model_DOI = [\"https://doi.org/10.1038/s41592-018-0261-2\",\"https://doi.org/10.1007/978-3-319-24574-4_28\", \"https://doi.org/10.1101/2020.03.20.000133\"]\n", + "# @markdown\n", "\n", "# Training data\n", "# ---------------------------------------\n", - "#@markdown ##Include information about training data (optional):\n", + "#@markdown ### Include information about training data (optional):\n", "include_training_data = False #@param {type: \"boolean\"}\n", - "#@markdown ### - If it is published in the BioImage Model Zoo, please, provide the ID\n", + "#@markdown #### If it is published in the BioImage Model Zoo, please, provide the ID\n", "data_from_bioimage_model_zoo = False #@param {type: \"boolean\"}\n", "training_data_ID = ''#@param {type:\"string\"}\n", - "#@markdown ### - If not, please provide the URL to the data and a short description to be added to the README.md file\n", + "#@markdown #### If not, please provide the URL to the data and a short description to be added to the README.md file\n", "training_data_source = ''#@param {type:\"string\"}\n", "training_data_description = ''#@param {type:\"string\"}\n", + "# @markdown\n", "\n", "# Add input image information\n", "# ---------------------------------------\n", - "#@markdown ##Indicate the minimum x/y size of the image (in pixels) and step size (in pixels) to be used for block/tiling:\n", + "#@markdown ### Minimum x/y size of the image and step size (in pixels) for block/tiling:\n", "# information about the example image\n", "min_size = 64 #@param {type:\"number\"}\n", "step_size = 16 #@param {type:\"number\"}\n", - "#@markdown ##Do you want to choose the example image?\n", + "# @markdown\n", + "\n", + "#@markdown ### Do you want to choose the example image?\n", "default_example_image = True #@param {type:\"boolean\"}\n", - "#@markdown ###If not, please input:\n", + "#@markdown #### If not, please input:\n", "fileID = \"\" #@param {type:\"string\"}\n", "if default_example_image:\n", " fileID = os.path.join(Source_QC_folder, os.listdir(Source_QC_folder)[0])\n", + "# @markdown\n", "\n", "# Load the model and process the example image\n", "# ---------------------------------------\n", @@ -2244,31 +2206,18 @@ " training_data = None\n", "\n", "# create the author/maintainer/packager spec input\n", - "author_1_spec = make_author(Trained_model_author_1)\n", - "authors = [author_1_spec]\n", + "authors = [] \n", + "for i in range(len(author_name.split(','))):\n", + " authors.append(bioimageio_spec.Author(name= author_name.split(',')[i].strip()))\n", "\n", - "# check if author 2 was filled\n", - "if 'Author 2 name' not in Trained_model_author_2:\n", - " author_2_spec = make_author(Trained_model_author_2)\n", - " authors.append(author_2_spec)\n", + "assert len(author_name.split(',')) >= Trained_model_packager, \"Author list has less authors than the packager number inserted.\"\n", + "packager = [authors[Trained_model_packager-1]]\n", "\n", - "if packager_same_as_author:\n", - " packager_spec = author_1_spec\n", - "else:\n", - " packager_spec = make_author(Trained_model_packager)\n", - "\n", - "if maintainer_same_as_author:\n", - " if author_1_spec.github_user != None:\n", - " maintainer_from_author = [str(author_1_spec.github_user), str(author_1_spec.name), str(author_1_spec.affiliation), str(author_1_spec.email), str(author_1_spec.orcid)]\n", - " maintainer_str = ', '.join(maintainer_from_author)\n", - " maintainer_spec = make_maintainer(maintainer_str)\n", - " else:\n", - " print('Please, provide the author GitHub username in the author information')\n", - "else:\n", - " maintainer_spec = make_maintainer(Trained_model_maintainer)\n", + "if len(author_name.split(',')) < maintainer_author_number:\n", + " print(\"Author list has less authors than the maintainer number inserted, no maintainer name will be added.\")\n", + "maintainer = [bioimageio_spec.Maintainer(github_user=Trained_model_maintainer, name=author_name.split(',')[maintainer_author_number-1].strip())]\n", "\n", - "\n", - "# I would recommend using CCBY-4 as licence\n", + "# I would recommend using CCBY-4 as license\n", "license = Trained_model_license\n", "\n", "# where to save the model\n", @@ -2401,8 +2350,8 @@ "plt.imsave(cover_path, cover, cmap='gray')\n", "\n", "# make weights description\n", - "unet_tf_weights = bioimageio_spec.KerasHdf5WeightsDescr(source=weight_path, tensorflow_version=tf.__version__)\n", - "unet_weights = bioimageio_spec.WeightsDescr(keras_hdf5=unet_tf_weights)\n", + "unet_keras_weights = bioimageio_spec.KerasHdf5WeightsDescr(source=weight_path, tensorflow_version=tf.__version__)\n", + "unet_weights = bioimageio_spec.WeightsDescr(keras_hdf5=unet_keras_weights)\n", "\n", "# create model description for export\n", "model_description = bioimageio_spec.ModelDescr(name=Trained_model_name,\n", @@ -2413,17 +2362,28 @@ " cite=citation_spec,\n", " license=license,\n", "\n", - " maintainers=[maintainer_spec],\n", + " maintainers=maintainer,\n", " tags=['zerocostdl4mic', 'deepimagej', 'segmentation', 'unet'],\n", " documentation= documentation_path,\n", " inputs=[input_tensor],\n", " outputs=[output_tensor],\n", - " packaged_by=[packager_spec],\n", + " packaged_by=packager,\n", " weights=unet_weights,\n", " training_data=training_data,\n", "\n", " )\n", "\n", + "# convert the keras weights to tensorflow and add them to the model\n", + "tf_weight_path = os.path.join(full_QC_model_path, \"tf_weights\")\n", + "# we need to make sure that the tf weight folder does not exist\n", + "if os.path.exists(tf_weight_path):\n", + " rmtree(Path(tf_weight_path))\n", + "convert_weights_to_tensorflow_saved_model_bundle(model_description, Path(tf_weight_path + \".zip\"))\n", + "\n", + "unet_tf_saved_model_bundle = bioimageio_spec.TensorflowSavedModelBundleWeightsDescr(source = Path(tf_weight_path + \".zip\"), tensorflow_version=tf.__version__)\n", + "\n", + "model_description.weights.tensorflow_saved_model_bundle = unet_tf_saved_model_bundle\n", + "\n", "\n", "# test model\n", "summary = bioimageio_core.test_model(model_description, weight_format=\"keras_hdf5\")\n", @@ -2588,6 +2548,11 @@ "# **7. Version log**\n", "\n", "---\n", + "**v2.1.4**: \n", + "\n", + "* Bug fixes and formatting\n", + "* Updated Bioimage.IO model export to latest version (core-0.6.10, spec-0.5.3.3)\n", + "\n", "**v2.1.3**: \n", "\n", "* Updated Bioimage.IO model export to latest version (core-0.6.9, spec-0.5.3.2)\n", @@ -2626,7 +2591,8 @@ "provenance": [] }, "kernelspec": { - "display_name": "Python 3", + "display_name": "bioimageio-core", + "language": "python", "name": "python3" }, "language_info": { @@ -2639,7 +2605,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.19" + "version": "3.12.3" } }, "nbformat": 4,