spacr 0.0.70__py3-none-any.whl → 0.0.71__py3-none-any.whl

{spacr-0.0.70.dist-info → spacr-0.0.71.dist-info}/RECORD

@@ -1,15 +1,14 @@
 spacr/__init__.py,sha256=64QJU2_IUd_40TTKQ2j239rF3PJP_gyciL_rolQOxuU,1144
 spacr/__main__.py,sha256=L3Dnk-YG3lULeaMxD1mS-_t89g4qWrJ7bnpBvNiQhUE,283
 spacr/alpha.py,sha256=Y95sLEfpK2OSYKRn3M8eUOU33JJeXfV8zhrC4KnwSTY,35244
-spacr/annotate_app.py,sha256=_KlDYbnaKr_VvghMWSr6gWbP_lByPghGLiCfEIJ48so,19500
+spacr/annotate_app.py,sha256=U7UfXEbXVAIdOc3X5ILEX2-3ac01JcwD-mIENdTh1q4,19478
 spacr/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
 spacr/cli.py,sha256=507jfOOEV8BoL4eeUcblvH-iiDHdBrEVJLu1ghAAPSc,1800
-spacr/core.py,sha256=EIhsuSyJQPxq1UfH3VNh3ubt403W1Ahvnz44pX35BCc,166307
+spacr/core.py,sha256=nZSOV1l72eO7ubJl1geTaQGONtdadhNK3GNY7BDaFWs,166179
 spacr/deep_spacr.py,sha256=ljIakns6q74an5QwDU7j0xoj6jRCAz-ejY0QHj9X0d8,33193
-spacr/foldseek.py,sha256=w7M7qRYvP5syJlPErQkHzPLOkiyLN77E0XyL3NiFZwI,33540
-spacr/get_alfafold_structures.py,sha256=n0g8gne-oyAV3Uo6qxZoJq5X1cUUyD8u0pOC_W2PX40,3541
+spacr/foldseek.py,sha256=YIP1d4Ci6CeA9jSyiv-HTDbNmAmcSM9Y_DaOs7wYzLY,33546
+spacr/get_alfafold_structures.py,sha256=ehx_MQgb12k3hFecP6cYVlm5TLO8iWjgevy8ESyS3cw,3544
 spacr/graph_learning.py,sha256=M7KW1J72LA4hLfVNVBOqxf_4z9tXi-UyoZfhaLJXqSE,11986
-spacr/graph_learning_lap.py,sha256=MyNRLb63gsjBlui-ByZ0anHugYulL6M-OsGm8rnGBmE,3385
 spacr/gui.py,sha256=zu-i8ezLJ03jNRACK7CRgNhkM8g8-pJFwZ-OSDFzsPg,6498
 spacr/gui_2.py,sha256=FPlmvGm1VIood_YBnG44IafgjjaVfagybTnjVEOs5Ig,3299
 spacr/gui_classify_app.py,sha256=LY33wott1mR7AFYwBI9ZQZYY16lBB-wuaY4pL_poaQ0,7884
@@ -17,23 +16,21 @@ spacr/gui_mask_app.py,sha256=WKkAH0jv-SnfaZdJ8MkC7mkUIVSSrNE8lUfH3QBvUak,9747
 spacr/gui_measure_app.py,sha256=5vjjds5NFaOcE8XeuWDug9k-NI4jbTrwp54sJ7DNaNI,9625
 spacr/gui_sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 spacr/gui_utils.py,sha256=JRWwmGEEVSPgs0UtZRukdNwIUJepbP675_Fvs5qocPk,49718
-spacr/io.py,sha256=8jpnsUOZMxfhGamduiq4BXgUtfh80kF4R_S-8N3EIrw,109305
+spacr/io.py,sha256=q6KWOvoM5d9SLfu0KJA9MB2a-R_QhQ6GaprmlkV2SH8,108463
 spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
 spacr/mask_app.py,sha256=jlKmj_evveIkkyH3PYEcAshcLXN0DOPWB1oc4hAwq9E,44201
 spacr/measure.py,sha256=KOBmrVE9nrKwIoXG16wV1sy5nSj9EOa_FhK7i431V-A,55325
 spacr/old_code.py,sha256=jw67DAGoLBd7mWofVzRJSEmCI1Qrff26zIo65SEkV00,13817
 spacr/plot.py,sha256=9tQEDDIHzex-T90VaS_PfcHwbWfYEYfMeKkgEdlK6ko,62045
 spacr/sequencing.py,sha256=OiRK6gpEkuEhKoUJcU-BXWDmz4RkDxKeJCE_C6w1zJc,50503
-spacr/sim.py,sha256=fpkOs-VBU40xBFuSoO97aTewQWPSYolg5C_PkjeQm_Y,71344
+spacr/sim.py,sha256=FveaVgBi3eypO2oVB5Dx-v0CC1Ny7UPfXkJiiRRodAk,71212
 spacr/timelapse.py,sha256=5TNmkzR_urMxy0eVB4quGdjNj2QduyiwrLL2I-udlAg,39614
-spacr/train.py,sha256=rpOJBu3ho0Oec37I1mO4_3eQ480y_4bgFiKCOgiyN8s,31741
-spacr/umap.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-spacr/utils.py,sha256=zX6zhS7UmCOA2JzBw4uDb-p0SPq5igaeYjzJ56d7hG8,171627
+spacr/utils.py,sha256=1RPGvCO2bl3a0LfiJ_8bZwJVWyXKI5hv51toahSZNZE,169827
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
-spacr-0.0.70.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.0.70.dist-info/METADATA,sha256=cE8tuT8BTSynUjv16YSLYPrcFq2Ngn17Hc7dxV5S2KE,4928
-spacr-0.0.70.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.0.70.dist-info/entry_points.txt,sha256=xncHsqD9MI5wj0_p4mgZlrB8dHm_g_qF0Ggo1c78LqY,315
-spacr-0.0.70.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.0.70.dist-info/RECORD,,
+spacr-0.0.71.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.0.71.dist-info/METADATA,sha256=GjQatvU0m5kUjGeE21ylp35mbauQHinUl2tqeGWHOpA,5121
+spacr-0.0.71.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.0.71.dist-info/entry_points.txt,sha256=xncHsqD9MI5wj0_p4mgZlrB8dHm_g_qF0Ggo1c78LqY,315
+spacr-0.0.71.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.0.71.dist-info/RECORD,,

spacr/graph_learning_lap.py

@@ -1,84 +0,0 @@
-import torch
-import torch.nn as nn
-import torch.nn.functional as F
-from torch.utils.data import Dataset, DataLoader, TensorDataset
-
-# Let's assume that the feature embedding part and the dataset loading part
-# has already been taken care of, and your data is already in the format
-# suitable for PyTorch (i.e., Tensors).
-
-class FeatureEmbedder(nn.Module):
-    def __init__(self, vocab_sizes, embedding_size):
-        super(FeatureEmbedder, self).__init__()
-        self.embeddings = nn.ModuleDict({
-            key: nn.Embedding(num_embeddings=vocab_size+1, 
-                              embedding_dim=embedding_size, 
-                              padding_idx=vocab_size)
-            for key, vocab_size in vocab_sizes.items()
-        })
-        # Adding the 'visit' embedding
-        self.embeddings['visit'] = nn.Parameter(torch.zeros(1, embedding_size))
-
-    def forward(self, feature_map, max_num_codes):
-        # Implementation will depend on how you want to handle sparse data
-        # This is just a placeholder
-        embeddings = {}
-        masks = {}
-        for key, tensor in feature_map.items():
-            embeddings[key] = self.embeddings[key](tensor.long())
-            mask = torch.ones_like(tensor, dtype=torch.float32)
-            masks[key] = mask.unsqueeze(-1)
-        
-        # Batch size hardcoded for simplicity in example
-        batch_size = 1  # Replace with actual batch size
-        embeddings['visit'] = self.embeddings['visit'].expand(batch_size, -1, -1)
-        masks['visit'] = torch.ones(batch_size, 1)
-        
-        return embeddings, masks
-
-class GraphConvolutionalTransformer(nn.Module):
-    def __init__(self, embedding_size=128, num_attention_heads=1, **kwargs):
-        super(GraphConvolutionalTransformer, self).__init__()
-        # Transformer Blocks
-        self.layers = nn.ModuleList([
-            nn.TransformerEncoderLayer(
-                d_model=embedding_size,
-                nhead=num_attention_heads,
-                batch_first=True) 
-            for _ in range(kwargs.get('num_transformer_stack', 3))
-        ])
-        # Output Layer for Classification
-        self.output_layer = nn.Linear(embedding_size, 1)
-
-    def feedforward(self, features, mask=None, training=None):
-        # Implement feedforward logic (placeholder)
-        pass
-
-    def forward(self, embeddings, masks, mask=None, training=False):
-        features = embeddings
-        attentions = []  # Storing attentions if needed
-        
-        # Pass through each Transformer block
-        for layer in self.layers:
-            features = layer(features)  # Apply transformer encoding here
-            
-            if mask is not None:
-                features = features * mask
-            
-        logits = self.output_layer(features[:, 0, :])  # Using the 'visit' embedding for classification
-        return logits, attentions
-
-# Usage Example
-vocab_sizes = {'dx_ints':3249, 'proc_ints':2210}
-embedding_size = 128
-gct_params = {
-    'embedding_size': embedding_size,
-    'num_transformer_stack': 3,
-    'num_attention_heads': 1
-}
-feature_embedder = FeatureEmbedder(vocab_sizes, embedding_size)
-gct_model = GraphConvolutionalTransformer(**gct_params)
-
-# Assume `feature_map` is a dictionary of tensors, and `max_num_codes` is provided
-embeddings, masks = feature_embedder(feature_map, max_num_codes)
-logits, attentions = gct_model(embeddings, masks)