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src/main/java/io/bioimage/modelrunner/model/stardist/Normalizer.java
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src/main/java/io/bioimage/modelrunner/model/stardist/StardistConfig.java
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src/main/java/io/bioimage/modelrunner/model/stardist/Utils.java
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src/main/java/io/bioimage/modelrunner/model/stardist_java_deprecate/Normalizer.java
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| package io.bioimage.modelrunner.model.stardist_java_deprecate; | ||
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| public class Normalizer { | ||
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| } |
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...e/modelrunner/model/stardist/Resizer.java → ...odel/stardist_java_deprecate/Resizer.java
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src/main/java/io/bioimage/modelrunner/model/stardist_java_deprecate/StardistConfig.java
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| /*- | ||
| * #%L | ||
| * Use deep learning frameworks from Java in an agnostic and isolated way. | ||
| * %% | ||
| * Copyright (C) 2022 - 2024 Institut Pasteur and BioImage.IO developers. | ||
| * %% | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| * #L% | ||
| */ | ||
| package io.bioimage.modelrunner.model.stardist_java_deprecate; | ||
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| import java.io.File; | ||
| import java.io.FileNotFoundException; | ||
| import java.io.IOException; | ||
| import java.util.Map; | ||
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| import io.bioimage.modelrunner.utils.JSONUtils; | ||
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| /** | ||
| * Implementation of the Stardist Config instance in Java. | ||
| * | ||
| *@author Carlos Garcia | ||
| */ | ||
| public class StardistConfig { | ||
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| final public int n_dim; | ||
| final public String axes; | ||
| final public int n_channel_in; | ||
| final public int n_channel_out; | ||
| final public String train_checkpoint; | ||
| final public String train_checkpoint_last; | ||
| final public String train_checkpoint_epoch; | ||
| final public int n_rays; | ||
| final public int[] grid; | ||
| final public String backbone; | ||
| final public int n_classes; | ||
| final public int unet_n_depth; | ||
| final public int[] unet_kernel_size; | ||
| final public int unet_n_filter_base; | ||
| final public int unet_n_conv_per_depth; | ||
| final public int[] unet_pool; | ||
| final public String unet_activation; | ||
| final public String unet_last_activation; | ||
| final public boolean unet_batch_norm; | ||
| final public double unet_dropout; | ||
| final public String unet_prefix; | ||
| final public int net_conv_after_unet; | ||
| final public int[] net_input_shape; | ||
| final public int[] net_mask_shape; | ||
| final public boolean train_shape_completion; | ||
| final public int train_completion_crop; | ||
| final public int[] train_patch_size; | ||
| final public float train_background_reg; | ||
| final public float train_foreground_only; | ||
| final public boolean train_sample_cache; | ||
| final public String train_dist_loss; | ||
| final public double[] train_loss_weights; | ||
| final public double[] train_class_weights; | ||
| final public int train_epochs; | ||
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| final public int train_steps_per_epoch; | ||
| final public double train_learning_rate; | ||
| final public int train_batch_size; | ||
| final public Integer train_n_val_patches; | ||
| final public boolean train_tensorboard; | ||
| final public Map<String, Object> train_reduce_lr; | ||
| final public int patience; | ||
| final public double min_delta; | ||
| final public double factor; | ||
| final public boolean use_gpu; | ||
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| public static final String FNAME = "config.json"; | ||
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| private StardistConfig(String path) throws IOException { | ||
| Map<String, Object> config = JSONUtils.load(path); | ||
| n_dim = (int) config.get("n_dim"); | ||
| axes = (String) config.get("axes"); | ||
| n_channel_in = (int) config.get("n_channel_in"); | ||
| n_channel_out = (int) config.get("n_channel_out"); | ||
| train_checkpoint = (String) config.get("train_checkpoint"); | ||
| train_checkpoint_last = (String) config.get("train_checkpoint_last"); | ||
| train_checkpoint_epoch = (String) config.get("train_checkpoint_epoch"); | ||
| n_rays = (int) config.get("n_rays"); | ||
| grid = (int[]) config.get("grid"); | ||
| backbone = (String) config.get("backbone"); | ||
| n_classes = (int) config.get("n_classes"); | ||
| unet_n_depth = (int) config.get("unet_n_depth"); | ||
| unet_kernel_size = (int[]) config.get("unet_kernel_size"); | ||
| unet_n_filter_base = (int) config.get("unet_n_filter_base"); | ||
| unet_n_conv_per_depth = (int) config.get("unet_n_conv_per_depth"); | ||
| unet_pool = (int[]) config.get("unet_pool"); | ||
| unet_activation = (String) config.get("unet_activation"); | ||
| unet_last_activation = (String) config.get("unet_last_activation"); | ||
| unet_batch_norm = (boolean) config.get("unet_batch_norm"); | ||
| unet_dropout = (double) config.get("unet_dropout"); | ||
| unet_prefix = (String) config.get("unet_prefix"); | ||
| net_conv_after_unet = (int) config.get("net_conv_after_unet"); | ||
| net_input_shape = (int[]) config.get("net_input_shape"); | ||
| net_mask_shape = (int[]) config.get("net_mask_shape"); | ||
| train_shape_completion = (boolean) config.get("train_shape_completion"); | ||
| train_completion_crop = (int) config.get("train_completion_crop"); | ||
| train_patch_size = (int[]) config.get("train_patch_size"); | ||
| train_background_reg = (float) config.get("train_background_reg"); | ||
| train_foreground_only = (float) config.get("train_foreground_only"); | ||
| train_sample_cache = (boolean) config.get("train_sample_cache"); | ||
| train_dist_loss = (String) config.get("train_dist_loss"); | ||
| train_loss_weights = (double[]) config.get("train_loss_weights"); | ||
| train_class_weights = (double[]) config.get("train_class_weights"); | ||
| train_epochs = (int) config.get("train_epochs"); | ||
| train_steps_per_epoch = (int) config.get("train_steps_per_epoch"); | ||
| train_learning_rate = (double) config.get("train_learning_rate"); | ||
| train_batch_size = (int) config.get("train_batch_size"); | ||
| train_n_val_patches = (Integer) config.get("train_n_val_patches"); | ||
| train_tensorboard = (boolean) config.get("train_tensorboard"); | ||
| train_reduce_lr = (Map<String, Object>) config.get("train_reduce_lr"); | ||
| use_gpu = (boolean) config.get("use_gpu"); | ||
| factor = (double) train_reduce_lr.get("factor"); | ||
| patience = (int) train_reduce_lr.get("patience"); | ||
| min_delta = (double) train_reduce_lr.get("min_delta"); | ||
| } | ||
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| public static StardistConfig create(String name, String baseDir) throws IOException { | ||
| if (new File(baseDir + File.separator + name + File.separator + FNAME).isFile() == false) | ||
| throw new IllegalArgumentException("No '" + FNAME + "' found at " + baseDir + File.separator + name); | ||
| return new StardistConfig(baseDir + File.separator + name + File.separator + FNAME); | ||
| } | ||
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| } |
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