spacr 0.0.70__py3-none-any.whl → 0.0.80__py3-none-any.whl

{spacr-0.0.70.dist-info → spacr-0.0.80.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.0.70
+Version: 0.0.80
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -9,7 +9,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
-Requires-Dist: dgl
+Requires-Dist: dgl ==0.9.1
 Requires-Dist: torch <3.0,>=2.2.1
 Requires-Dist: torchvision <1.0,>=0.17.1
 Requires-Dist: torch-geometric <3.0,>=2.5.1
@@ -46,6 +46,8 @@ Requires-Dist: opencv-python ; extra == 'full'
 Provides-Extra: headless
 Requires-Dist: opencv-python-headless ; extra == 'headless'
 
+.. |Documentation Status| image:: https://readthedocs.org/projects/spacr/badge/?version=latest
+   :target: https://spacr.readthedocs.io/en/latest/?badge=latest
 .. |PyPI version| image:: https://badge.fury.io/py/spacr.svg
    :target: https://badge.fury.io/py/spacr
 .. |Python version| image:: https://img.shields.io/pypi/pyversions/spacr
@@ -55,25 +57,25 @@ Requires-Dist: opencv-python-headless ; extra == 'headless'
 .. |repo size| image:: https://img.shields.io/github/repo-size/EinarOlafsson/spacr
    :target: https://github.com/EinarOlafsson/spacr/
 
-|PyPI version| |Python version| |Licence: GPL v3| |repo size|
+|Documentation Status| |PyPI version| |Python version| |Licence: GPL v3| |repo size|
 
 SpaCr
 =====
 
-Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understand host clearance mechanisms and how pathogens evade them. Spacr is a Python-based software package for generating single cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. Spacr provides a flexible toolset to extract single cell images and measurements from high content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate and analyze pooled CRISPR-Cas9 imaging screens.
+Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understand host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
 
 Features
 --------
 
 -  **Generate Masks:** Generate cellpose masks of cell, nuclei, and pathogen objects.
 
--  **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity percentiles, shannon-entropy, pearsons and manders correlations, homogeneity and radial distribution. Measurements are saved to a SQL database in object level tables.
+-  **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity percentiles, shannon-entropy, pearsons and manders correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
 
--  **Crop Images:** Objects (e.g. cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in a SQL database that can be annotated and used to train CNNs/Transformer models for classification tasks.
+-  **Crop Images:** Objects (e.g., cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in a SQL database that can be annotated and used to train CNNs/Transformer models for classification tasks.
 
 -  **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing.
 
--  **Manual Annotation:** Supports manual annotation of single cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
+-  **Manual Annotation:** Supports manual annotation of single-cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
 
 -  **Finetune Cellpose Models:** Adjust pre-existing Cellpose models to your specific dataset for improved performance.
 
@@ -93,7 +95,7 @@ Requires Tkinter for graphical user interface features.
 Ubuntu
 ~~~~~~
 
-Before installing spacr, ensure Tkinter is installed:
+Before installing SpaCr, ensure Tkinter is installed:
 
 (Tkinter is included with the standard Python installation on macOS, and Windows)
 

spacr-0.0.80.dist-info/RECORD

@@ -0,0 +1,36 @@
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+spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
+spacr/alpha.py,sha256=Y95sLEfpK2OSYKRn3M8eUOU33JJeXfV8zhrC4KnwSTY,35244
+spacr/annotate_app.py,sha256=w7t7Zilu31FSIRDKtIPae8X4MZGez3cJugFM3rOmnlQ,20617
+spacr/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
+spacr/cli.py,sha256=507jfOOEV8BoL4eeUcblvH-iiDHdBrEVJLu1ghAAPSc,1800
+spacr/core.py,sha256=CHtBCYnx-oIU7f78X8QBMrVtHtaU0Dwu12zpYouUa7E,155454
+spacr/deep_spacr.py,sha256=ljIakns6q74an5QwDU7j0xoj6jRCAz-ejY0QHj9X0d8,33193
+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
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+spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
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+spacr/old_code.py,sha256=jw67DAGoLBd7mWofVzRJSEmCI1Qrff26zIo65SEkV00,13817
+spacr/plot.py,sha256=fnswxUXHwSLmxRpqSAmoUl5ln-_ueYPeYQlDmiYSwzQ,63299
+spacr/sequencing.py,sha256=TWQtylArdWZCYcjYrvfy7AAZdVprCMwXc1WMEavw10E,50987
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+spacr/timelapse.py,sha256=5TNmkzR_urMxy0eVB4quGdjNj2QduyiwrLL2I-udlAg,39614
+spacr/utils.py,sha256=3cA3qUNf7l_VEeuhype2kI7B5IoYK0hb6Y31Q6Si3ds,184107
+spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
+spacr/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
+spacr-0.0.80.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.0.80.dist-info/METADATA,sha256=ZvBlLVEEUqE0JiUTbokhpMPI33nHAzvY2Ahmg1WueLk,5121
+spacr-0.0.80.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.0.80.dist-info/entry_points.txt,sha256=xncHsqD9MI5wj0_p4mgZlrB8dHm_g_qF0Ggo1c78LqY,315
+spacr-0.0.80.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.0.80.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)