docs update

docs/addnew_link.rst

@@ -1,9 +1,9 @@
---------------------------------
+----------------------------------
 Add new modalities to the package
---------------------------------
+----------------------------------
 
 .. include:: add_dset.md
   :parser: myst_parser.sphinx_
 
 .. include:: add_model.md
-  :parser: myst_parser.sphinx_
+  :parser: myst_parser.sphinx_

docs/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 9cbfd784c44dece22d4641a9a6917821
+config: 20f95c4bc15d6a49391157c342a6fdb8
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_modules/domid/algos/builder_ae.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/algos/builder_dec.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/algos/builder_m2yd.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/algos/builder_sdcn.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>
@@ -347,6 +349,7 @@ <h1 id="modules-domid-algos-builder-sdcn--page-root">Source code for domid.algos
             model_method=args.model_method,
             pre_tr_weight_path=args.pre_tr_weight_path,
             feat_extract=args.feat_extract,
+            graph_method=args.graph_method,
         )
 
         observer = ObVisitorCleanUp(

docs/build/html/_modules/domid/algos/builder_vade.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/arg_parser.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/compos/DEC_clustering_layer.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/compos/GNN.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/compos/GNN_layer.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/compos/VAE_blocks.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/compos/cnn_AE.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/compos/cnn_VAE.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/compos/linear_AE.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/compos/linear_VAE.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/compos/nn_net.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/compos/predict_basic.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/compos/tensorboard_fun.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>
@@ -325,7 +327,7 @@ <h1 id="modules-domid-compos-tensorboard-fun--page-root">Source code for domid.c
     inject_tensor=None,
     other_info=None,
 ):
-    if lr &gt; 2:
+    if lr &gt; 0:
         writer.add_scalar("learning rate", lr, epoch)
         writer.add_scalar("warmup", warmup_beta, epoch)
         if not pretraining_finished:

docs/build/html/_modules/domid/dsets/a_dset_mnist_color_rgb_solo.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/dsets/dset_her2.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/dsets/dset_mnist.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/dsets/dset_mnist_color_solo_default.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/dsets/dset_unittest.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/dsets/dset_usps.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/dsets/dset_wsi.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/dsets/generate_dataset_dataframe_her2.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/dsets/make_graph.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/dsets/make_graph_wsi.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/models/a_model_cluster.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/models/model_ae.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>
@@ -417,7 +419,7 @@ <h1 id="modules-domid-models-model-ae--page-root">Source code for domid.models.m
             enc_h1, enc_h2, enc_h3, z = self.encoder(x)
             # _, _, z, *_ = self._inference(x)
 
-            kmeans = KMeans(n_clusters=self.d_dim, n_init=20)
+            kmeans = KMeans(n_clusters=self.d_dim)
 
             kmeans.fit_predict(z.detach().cpu().numpy())
             # x_bar, *_ = self.decoder(z)

docs/build/html/_modules/domid/models/model_dec.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>
@@ -453,7 +455,9 @@ <h1 id="modules-domid-models-model-dec--page-root">Source code for domid.models.
                 zy = results[2]
 
             x_pro, *_ = self.decoder(zy)
-            preds, probs, z, z_mu, z_sigma2_log, mu_c, log_sigma2_c, pi, logits = (r.cpu().detach() for r in results)
+            preds, probs, z, z_mu, z_sigma2_log, mu_c, log_sigma2_c, pi, logits = (
+                r.cpu().detach() if r is not None else None for r in results
+            )
             return preds, z_mu, z, log_sigma2_c, probs, x_pro
 
         def _cal_kl_loss(self, x, inject_tensor, warmup_beta=0.1):

docs/build/html/_modules/domid/models/model_m2yd.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>

docs/build/html/_modules/domid/models/model_sdcn.html

@@ -166,6 +166,8 @@
             <li class="md-tabs__item"><a href="../../../about_link.html" class="md-tabs__link">About</a></li>
 
             <li class="md-tabs__item"><a href="../../../readme_link.html" class="md-tabs__link">Quick Start</a></li>
+
+            <li class="md-tabs__item"><a href="../../../addnew_link.html" class="md-tabs__link">Custom Datasets and Models</a></li>
           <li class="md-tabs__item"><a href="../../index.html" class="md-tabs__link">Module code</a></li>
       </ul>
     </div>
@@ -346,7 +348,7 @@ <h1 id="modules-domid-models-model-sdcn--page-root">Source code for domid.models
             dim_inject_y=0,
             pre_tr_weight_path=None,
             feat_extract="vae",
-            graph_method="heat",
+            graph_method=None,
         ):
 
             super(ModelSDCN, self).__init__()
@@ -441,7 +443,7 @@ <h1 id="modules-domid-models-model-sdcn--page-root">Source code for domid.models
                 self.graph_method = "heat"
             if "wsi" in self.task:
                 self.graph_method = "patch_distance"
-            if self.graph_method is not None:
+            if graph_method is not None:
                 self.graph_method = graph_method
 
             if self.task == "wsi":