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-

cyto_dl.api package#

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cyto_dl.api package#

Subpackages#

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C

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  • - cyto_dl.api - -
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    C

  • module
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    • cyto_dl.models.classification.timepoint_classification @@ -1029,6 +1020,8 @@

      C

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    • cyto_dl.models.contrastive @@ -2259,8 +2252,6 @@

      M

      • cyto_dl -
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      • cyto_dl.api
      • cyto_dl.api.cyto_dl_model
      • diff --git a/objects.inv b/objects.inv index 5cd7cbf5..388ce4ac 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/py-modindex.html b/py-modindex.html index 87496dc5..1c2735a1 100644 --- a/py-modindex.html +++ b/py-modindex.html @@ -457,12 +457,6 @@

        Python Module Index

        cyto_dl - - -     - cyto_dl.api - -     diff --git a/searchindex.js b/searchindex.js index c76d6d5b..3c1a3086 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["api", "cyto_dl", "cyto_dl.api", "cyto_dl.api.cyto_dl_model", "cyto_dl.api.cyto_dl_model.cyto_dl_base_model", "cyto_dl.api.cyto_dl_model.segmentation_plugin_model", "cyto_dl.api.data", "cyto_dl.api.model", "cyto_dl.callbacks", "cyto_dl.callbacks.callback_utils", "cyto_dl.callbacks.csv_saver", "cyto_dl.callbacks.image_saver", "cyto_dl.callbacks.latent_walk", "cyto_dl.callbacks.layer_freeze", "cyto_dl.callbacks.model_utils", "cyto_dl.callbacks.outlier_detection", "cyto_dl.compile", "cyto_dl.dataframe", "cyto_dl.dataframe.readers", "cyto_dl.dataframe.transforms", "cyto_dl.dataframe.transforms.filter", "cyto_dl.dataframe.transforms.group_cols", "cyto_dl.dataframe.transforms.misc", "cyto_dl.dataframe.transforms.split", "cyto_dl.datamodules", "cyto_dl.datamodules.array", "cyto_dl.datamodules.data_dict", "cyto_dl.datamodules.dataframe", "cyto_dl.datamodules.dataframe.dataframe_datamodule", "cyto_dl.datamodules.dataframe.grouped_dataframe_datamodule", "cyto_dl.datamodules.dataframe.utils", "cyto_dl.datamodules.folder", "cyto_dl.datamodules.multidim_image", "cyto_dl.datamodules.smartcache", "cyto_dl.datamodules.torchvision", "cyto_dl.eval", "cyto_dl.image", "cyto_dl.image.io", "cyto_dl.image.io.aicsimage_loader", "cyto_dl.image.io.monai_bio_reader", "cyto_dl.image.io.numpy_reader", "cyto_dl.image.io.ome_zarr_reader", "cyto_dl.image.io.polygon_loader", "cyto_dl.image.io.skimage_reader", "cyto_dl.image.transforms", "cyto_dl.image.transforms.add_meta", "cyto_dl.image.transforms.bright_sampler", "cyto_dl.image.transforms.clip", "cyto_dl.image.transforms.contrastadjust", "cyto_dl.image.transforms.generate_jepa_masks", "cyto_dl.image.transforms.merge", "cyto_dl.image.transforms.multiscale_cropper", "cyto_dl.image.transforms.pad", "cyto_dl.image.transforms.project", "cyto_dl.image.transforms.rotation_mask_transform", "cyto_dl.image.transforms.save", "cyto_dl.image.transforms.so2_random_rotation", "cyto_dl.image.transforms.track_transforms", "cyto_dl.loggers", "cyto_dl.loggers.mlflow", "cyto_dl.models", "cyto_dl.models.base_model", "cyto_dl.models.basic_model", "cyto_dl.models.classification", "cyto_dl.models.classification.classification", "cyto_dl.models.classification.timepoint_classification", "cyto_dl.models.contrastive", "cyto_dl.models.contrastive.contrastive", "cyto_dl.models.handlers", "cyto_dl.models.handlers.base_handler", "cyto_dl.models.handlers.image_handler", "cyto_dl.models.handlers.load_image_patch", "cyto_dl.models.im2im", "cyto_dl.models.im2im.gan", "cyto_dl.models.im2im.multi_task", "cyto_dl.models.im2im.utils", "cyto_dl.models.im2im.utils.instance_seg", "cyto_dl.models.im2im.utils.noise_annealer", "cyto_dl.models.im2im.utils.postprocessing", "cyto_dl.models.im2im.utils.postprocessing.act_thresh_label", "cyto_dl.models.im2im.utils.postprocessing.auto_thresh", "cyto_dl.models.im2im.utils.postprocessing.dict_to_im", "cyto_dl.models.jepa", "cyto_dl.models.jepa.ijepa", "cyto_dl.models.jepa.iwm", "cyto_dl.models.jepa.jepa_base", "cyto_dl.models.utils", "cyto_dl.models.utils.mlflow", "cyto_dl.models.utils.utils", "cyto_dl.models.vae", "cyto_dl.models.vae.base_vae", "cyto_dl.models.vae.image_canon_vae", "cyto_dl.models.vae.image_encoder", "cyto_dl.models.vae.image_vae", "cyto_dl.models.vae.latent_loss_vae", "cyto_dl.models.vae.o2_spharm_vae", "cyto_dl.models.vae.o2_spharm_vae.o2_spharm_encoder", "cyto_dl.models.vae.o2_spharm_vae.o2_spharm_vae", "cyto_dl.models.vae.point_cloud_vae", "cyto_dl.models.vae.priors", "cyto_dl.models.vae.priors.abstract_prior", "cyto_dl.models.vae.priors.gaussian", "cyto_dl.models.vae.priors.identity_prior", "cyto_dl.models.vae.priors.joint_prior", "cyto_dl.models.vae.tabular_vae", "cyto_dl.nn", "cyto_dl.nn.discriminators", "cyto_dl.nn.discriminators.multi_scale_discriminator", "cyto_dl.nn.discriminators.n_layer_discriminator", "cyto_dl.nn.head", "cyto_dl.nn.head.base_head", "cyto_dl.nn.head.gan_head", "cyto_dl.nn.head.gan_head_superres", "cyto_dl.nn.head.mae_head", "cyto_dl.nn.head.mask_head", "cyto_dl.nn.head.res_blocks_head", "cyto_dl.nn.head.vic_reg", "cyto_dl.nn.hr_skip", "cyto_dl.nn.losses", "cyto_dl.nn.losses.adversarial_loss", "cyto_dl.nn.losses.chamfer_loss", "cyto_dl.nn.losses.continuous_bernoulli", "cyto_dl.nn.losses.cosine_loss", "cyto_dl.nn.losses.gan_loss", "cyto_dl.nn.losses.gaussian_nll_loss", "cyto_dl.nn.losses.geomloss", "cyto_dl.nn.losses.loss_wrapper", "cyto_dl.nn.losses.spharm_loss", "cyto_dl.nn.losses.threshold_loss", "cyto_dl.nn.losses.vic_reg", "cyto_dl.nn.losses.weibull", "cyto_dl.nn.losses.weighted_mse_loss", "cyto_dl.nn.mlp", "cyto_dl.nn.point_cloud", "cyto_dl.nn.point_cloud.dgcnn", "cyto_dl.nn.point_cloud.folding_net", "cyto_dl.nn.point_cloud.graph_functions", "cyto_dl.nn.point_cloud.vnn", "cyto_dl.nn.res_unit", "cyto_dl.nn.spatial_transformer", "cyto_dl.nn.track_sequence_predictor", "cyto_dl.nn.vits", "cyto_dl.nn.vits.blocks", "cyto_dl.nn.vits.blocks.cross_attention", "cyto_dl.nn.vits.blocks.intermediate_weigher", "cyto_dl.nn.vits.blocks.masked_unit_attention", "cyto_dl.nn.vits.blocks.patchify", "cyto_dl.nn.vits.blocks.patchify.patchify", "cyto_dl.nn.vits.blocks.patchify.patchify_base", "cyto_dl.nn.vits.blocks.patchify.patchify_hiera", "cyto_dl.nn.vits.decoder", "cyto_dl.nn.vits.encoder", "cyto_dl.nn.vits.mae", "cyto_dl.nn.vits.predictor", "cyto_dl.nn.vits.seg", "cyto_dl.nn.vits.utils", "cyto_dl.point_cloud", "cyto_dl.point_cloud.io", "cyto_dl.point_cloud.io.read_pcloud", "cyto_dl.train", "cyto_dl.utils", "cyto_dl.utils.array", "cyto_dl.utils.checkpoint", "cyto_dl.utils.config", "cyto_dl.utils.download_test_data", "cyto_dl.utils.dummy_dataset", "cyto_dl.utils.pylogger", "cyto_dl.utils.rich_utils", "cyto_dl.utils.rotation", "cyto_dl.utils.spharm", "cyto_dl.utils.spharm.reconstruction", "cyto_dl.utils.spharm.rotation", "cyto_dl.utils.template_utils", "index", "installation", "modules", "overview", "using_examples"], "filenames": ["api.rst", "cyto_dl.rst", "cyto_dl.api.rst", "cyto_dl.api.cyto_dl_model.rst", "cyto_dl.api.cyto_dl_model.cyto_dl_base_model.rst", "cyto_dl.api.cyto_dl_model.segmentation_plugin_model.rst", "cyto_dl.api.data.rst", "cyto_dl.api.model.rst", "cyto_dl.callbacks.rst", "cyto_dl.callbacks.callback_utils.rst", "cyto_dl.callbacks.csv_saver.rst", "cyto_dl.callbacks.image_saver.rst", "cyto_dl.callbacks.latent_walk.rst", "cyto_dl.callbacks.layer_freeze.rst", "cyto_dl.callbacks.model_utils.rst", "cyto_dl.callbacks.outlier_detection.rst", "cyto_dl.compile.rst", "cyto_dl.dataframe.rst", "cyto_dl.dataframe.readers.rst", "cyto_dl.dataframe.transforms.rst", "cyto_dl.dataframe.transforms.filter.rst", "cyto_dl.dataframe.transforms.group_cols.rst", "cyto_dl.dataframe.transforms.misc.rst", "cyto_dl.dataframe.transforms.split.rst", "cyto_dl.datamodules.rst", "cyto_dl.datamodules.array.rst", "cyto_dl.datamodules.data_dict.rst", "cyto_dl.datamodules.dataframe.rst", "cyto_dl.datamodules.dataframe.dataframe_datamodule.rst", "cyto_dl.datamodules.dataframe.grouped_dataframe_datamodule.rst", "cyto_dl.datamodules.dataframe.utils.rst", "cyto_dl.datamodules.folder.rst", "cyto_dl.datamodules.multidim_image.rst", "cyto_dl.datamodules.smartcache.rst", "cyto_dl.datamodules.torchvision.rst", "cyto_dl.eval.rst", "cyto_dl.image.rst", "cyto_dl.image.io.rst", "cyto_dl.image.io.aicsimage_loader.rst", "cyto_dl.image.io.monai_bio_reader.rst", "cyto_dl.image.io.numpy_reader.rst", "cyto_dl.image.io.ome_zarr_reader.rst", "cyto_dl.image.io.polygon_loader.rst", "cyto_dl.image.io.skimage_reader.rst", "cyto_dl.image.transforms.rst", "cyto_dl.image.transforms.add_meta.rst", "cyto_dl.image.transforms.bright_sampler.rst", "cyto_dl.image.transforms.clip.rst", "cyto_dl.image.transforms.contrastadjust.rst", "cyto_dl.image.transforms.generate_jepa_masks.rst", "cyto_dl.image.transforms.merge.rst", "cyto_dl.image.transforms.multiscale_cropper.rst", "cyto_dl.image.transforms.pad.rst", "cyto_dl.image.transforms.project.rst", "cyto_dl.image.transforms.rotation_mask_transform.rst", "cyto_dl.image.transforms.save.rst", "cyto_dl.image.transforms.so2_random_rotation.rst", "cyto_dl.image.transforms.track_transforms.rst", "cyto_dl.loggers.rst", "cyto_dl.loggers.mlflow.rst", "cyto_dl.models.rst", "cyto_dl.models.base_model.rst", "cyto_dl.models.basic_model.rst", "cyto_dl.models.classification.rst", "cyto_dl.models.classification.classification.rst", "cyto_dl.models.classification.timepoint_classification.rst", "cyto_dl.models.contrastive.rst", "cyto_dl.models.contrastive.contrastive.rst", "cyto_dl.models.handlers.rst", "cyto_dl.models.handlers.base_handler.rst", "cyto_dl.models.handlers.image_handler.rst", "cyto_dl.models.handlers.load_image_patch.rst", "cyto_dl.models.im2im.rst", "cyto_dl.models.im2im.gan.rst", "cyto_dl.models.im2im.multi_task.rst", "cyto_dl.models.im2im.utils.rst", "cyto_dl.models.im2im.utils.instance_seg.rst", "cyto_dl.models.im2im.utils.noise_annealer.rst", "cyto_dl.models.im2im.utils.postprocessing.rst", "cyto_dl.models.im2im.utils.postprocessing.act_thresh_label.rst", "cyto_dl.models.im2im.utils.postprocessing.auto_thresh.rst", "cyto_dl.models.im2im.utils.postprocessing.dict_to_im.rst", "cyto_dl.models.jepa.rst", "cyto_dl.models.jepa.ijepa.rst", "cyto_dl.models.jepa.iwm.rst", "cyto_dl.models.jepa.jepa_base.rst", "cyto_dl.models.utils.rst", "cyto_dl.models.utils.mlflow.rst", "cyto_dl.models.utils.utils.rst", "cyto_dl.models.vae.rst", "cyto_dl.models.vae.base_vae.rst", "cyto_dl.models.vae.image_canon_vae.rst", "cyto_dl.models.vae.image_encoder.rst", "cyto_dl.models.vae.image_vae.rst", "cyto_dl.models.vae.latent_loss_vae.rst", "cyto_dl.models.vae.o2_spharm_vae.rst", "cyto_dl.models.vae.o2_spharm_vae.o2_spharm_encoder.rst", "cyto_dl.models.vae.o2_spharm_vae.o2_spharm_vae.rst", "cyto_dl.models.vae.point_cloud_vae.rst", "cyto_dl.models.vae.priors.rst", "cyto_dl.models.vae.priors.abstract_prior.rst", "cyto_dl.models.vae.priors.gaussian.rst", "cyto_dl.models.vae.priors.identity_prior.rst", "cyto_dl.models.vae.priors.joint_prior.rst", "cyto_dl.models.vae.tabular_vae.rst", "cyto_dl.nn.rst", "cyto_dl.nn.discriminators.rst", "cyto_dl.nn.discriminators.multi_scale_discriminator.rst", "cyto_dl.nn.discriminators.n_layer_discriminator.rst", "cyto_dl.nn.head.rst", "cyto_dl.nn.head.base_head.rst", "cyto_dl.nn.head.gan_head.rst", "cyto_dl.nn.head.gan_head_superres.rst", "cyto_dl.nn.head.mae_head.rst", "cyto_dl.nn.head.mask_head.rst", "cyto_dl.nn.head.res_blocks_head.rst", "cyto_dl.nn.head.vic_reg.rst", "cyto_dl.nn.hr_skip.rst", "cyto_dl.nn.losses.rst", "cyto_dl.nn.losses.adversarial_loss.rst", "cyto_dl.nn.losses.chamfer_loss.rst", "cyto_dl.nn.losses.continuous_bernoulli.rst", "cyto_dl.nn.losses.cosine_loss.rst", "cyto_dl.nn.losses.gan_loss.rst", "cyto_dl.nn.losses.gaussian_nll_loss.rst", "cyto_dl.nn.losses.geomloss.rst", "cyto_dl.nn.losses.loss_wrapper.rst", "cyto_dl.nn.losses.spharm_loss.rst", "cyto_dl.nn.losses.threshold_loss.rst", "cyto_dl.nn.losses.vic_reg.rst", "cyto_dl.nn.losses.weibull.rst", "cyto_dl.nn.losses.weighted_mse_loss.rst", "cyto_dl.nn.mlp.rst", "cyto_dl.nn.point_cloud.rst", "cyto_dl.nn.point_cloud.dgcnn.rst", "cyto_dl.nn.point_cloud.folding_net.rst", "cyto_dl.nn.point_cloud.graph_functions.rst", "cyto_dl.nn.point_cloud.vnn.rst", "cyto_dl.nn.res_unit.rst", "cyto_dl.nn.spatial_transformer.rst", "cyto_dl.nn.track_sequence_predictor.rst", "cyto_dl.nn.vits.rst", "cyto_dl.nn.vits.blocks.rst", "cyto_dl.nn.vits.blocks.cross_attention.rst", "cyto_dl.nn.vits.blocks.intermediate_weigher.rst", "cyto_dl.nn.vits.blocks.masked_unit_attention.rst", "cyto_dl.nn.vits.blocks.patchify.rst", "cyto_dl.nn.vits.blocks.patchify.patchify.rst", "cyto_dl.nn.vits.blocks.patchify.patchify_base.rst", "cyto_dl.nn.vits.blocks.patchify.patchify_hiera.rst", "cyto_dl.nn.vits.decoder.rst", "cyto_dl.nn.vits.encoder.rst", "cyto_dl.nn.vits.mae.rst", "cyto_dl.nn.vits.predictor.rst", "cyto_dl.nn.vits.seg.rst", "cyto_dl.nn.vits.utils.rst", "cyto_dl.point_cloud.rst", "cyto_dl.point_cloud.io.rst", "cyto_dl.point_cloud.io.read_pcloud.rst", "cyto_dl.train.rst", "cyto_dl.utils.rst", "cyto_dl.utils.array.rst", "cyto_dl.utils.checkpoint.rst", "cyto_dl.utils.config.rst", "cyto_dl.utils.download_test_data.rst", "cyto_dl.utils.dummy_dataset.rst", "cyto_dl.utils.pylogger.rst", "cyto_dl.utils.rich_utils.rst", "cyto_dl.utils.rotation.rst", "cyto_dl.utils.spharm.rst", "cyto_dl.utils.spharm.reconstruction.rst", "cyto_dl.utils.spharm.rotation.rst", "cyto_dl.utils.template_utils.rst", "index.rst", "installation.rst", "modules.rst", "overview.md", "using_examples.rst"], "titles": ["Using the API", "cyto_dl package", "cyto_dl.api package", "cyto_dl.api.cyto_dl_model package", "cyto_dl.api.cyto_dl_model.cyto_dl_base_model module", "cyto_dl.api.cyto_dl_model.segmentation_plugin_model module", "cyto_dl.api.data module", "cyto_dl.api.model module", "cyto_dl.callbacks package", "cyto_dl.callbacks.callback_utils module", "cyto_dl.callbacks.csv_saver module", "cyto_dl.callbacks.image_saver module", "cyto_dl.callbacks.latent_walk module", "cyto_dl.callbacks.layer_freeze module", "cyto_dl.callbacks.model_utils module", "cyto_dl.callbacks.outlier_detection module", "cyto_dl.compile module", "cyto_dl.dataframe package", "cyto_dl.dataframe.readers module", "cyto_dl.dataframe.transforms package", "cyto_dl.dataframe.transforms.filter module", "cyto_dl.dataframe.transforms.group_cols module", "cyto_dl.dataframe.transforms.misc module", "cyto_dl.dataframe.transforms.split module", "cyto_dl.datamodules package", "cyto_dl.datamodules.array module", "cyto_dl.datamodules.data_dict module", "cyto_dl.datamodules.dataframe package", "cyto_dl.datamodules.dataframe.dataframe_datamodule module", "cyto_dl.datamodules.dataframe.grouped_dataframe_datamodule module", "cyto_dl.datamodules.dataframe.utils module", "cyto_dl.datamodules.folder module", "cyto_dl.datamodules.multidim_image module", "cyto_dl.datamodules.smartcache module", "cyto_dl.datamodules.torchvision module", "cyto_dl.eval module", "cyto_dl.image package", "cyto_dl.image.io package", "cyto_dl.image.io.aicsimage_loader module", "cyto_dl.image.io.monai_bio_reader module", "cyto_dl.image.io.numpy_reader module", "cyto_dl.image.io.ome_zarr_reader module", "cyto_dl.image.io.polygon_loader module", "cyto_dl.image.io.skimage_reader module", "cyto_dl.image.transforms package", "cyto_dl.image.transforms.add_meta module", "cyto_dl.image.transforms.bright_sampler module", "cyto_dl.image.transforms.clip module", "cyto_dl.image.transforms.contrastadjust module", "cyto_dl.image.transforms.generate_jepa_masks module", "cyto_dl.image.transforms.merge module", "cyto_dl.image.transforms.multiscale_cropper module", "cyto_dl.image.transforms.pad module", "cyto_dl.image.transforms.project module", "cyto_dl.image.transforms.rotation_mask_transform module", "cyto_dl.image.transforms.save module", "cyto_dl.image.transforms.so2_random_rotation module", "cyto_dl.image.transforms.track_transforms module", "cyto_dl.loggers package", "cyto_dl.loggers.mlflow module", "cyto_dl.models package", "cyto_dl.models.base_model module", "cyto_dl.models.basic_model module", "cyto_dl.models.classification package", "cyto_dl.models.classification.classification module", "cyto_dl.models.classification.timepoint_classification module", "cyto_dl.models.contrastive package", "cyto_dl.models.contrastive.contrastive module", "cyto_dl.models.handlers package", "cyto_dl.models.handlers.base_handler module", "cyto_dl.models.handlers.image_handler module", "cyto_dl.models.handlers.load_image_patch module", "cyto_dl.models.im2im package", "cyto_dl.models.im2im.gan module", "cyto_dl.models.im2im.multi_task module", "cyto_dl.models.im2im.utils package", "cyto_dl.models.im2im.utils.instance_seg module", "cyto_dl.models.im2im.utils.noise_annealer module", "cyto_dl.models.im2im.utils.postprocessing package", "cyto_dl.models.im2im.utils.postprocessing.act_thresh_label module", "cyto_dl.models.im2im.utils.postprocessing.auto_thresh module", "cyto_dl.models.im2im.utils.postprocessing.dict_to_im module", "cyto_dl.models.jepa package", "cyto_dl.models.jepa.ijepa module", "cyto_dl.models.jepa.iwm module", "cyto_dl.models.jepa.jepa_base module", "cyto_dl.models.utils package", "cyto_dl.models.utils.mlflow module", "cyto_dl.models.utils.utils module", "cyto_dl.models.vae package", "cyto_dl.models.vae.base_vae module", "cyto_dl.models.vae.image_canon_vae module", "cyto_dl.models.vae.image_encoder module", "cyto_dl.models.vae.image_vae module", "cyto_dl.models.vae.latent_loss_vae module", "cyto_dl.models.vae.o2_spharm_vae 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