spacr 0.5.0__py3-none-any.whl → 0.9.0__py3-none-any.whl

spacr/resources/MEDIAR/train_tools/models/MEDIARFormer.py

@@ -1,102 +0,0 @@
-import torch
-import torch.nn as nn
-
-from segmentation_models_pytorch import MAnet
-from segmentation_models_pytorch.base.modules import Activation
-
-__all__ = ["MEDIARFormer"]
-
-
-class MEDIARFormer(MAnet):
-    """MEDIAR-Former Model"""
-
-    def __init__(
-        self,
-        encoder_name="mit_b5",  # Default encoder
-        encoder_weights="imagenet",  # Pre-trained weights
-        decoder_channels=(1024, 512, 256, 128, 64),  # Decoder configuration
-        decoder_pab_channels=256,  # Decoder Pyramid Attention Block channels
-        in_channels=3,  # Number of input channels
-        classes=3,  # Number of output classes
-    ):
-        # Initialize the MAnet model with provided parameters
-        super().__init__(
-            encoder_name=encoder_name,
-            encoder_weights=encoder_weights,
-            decoder_channels=decoder_channels,
-            decoder_pab_channels=decoder_pab_channels,
-            in_channels=in_channels,
-            classes=classes,
-        )
-
-        # Remove the default segmentation head as it's not used in this architecture
-        self.segmentation_head = None
-
-        # Modify all activation functions in the encoder and decoder from ReLU to Mish
-        _convert_activations(self.encoder, nn.ReLU, nn.Mish(inplace=True))
-        _convert_activations(self.decoder, nn.ReLU, nn.Mish(inplace=True))
-
-        # Add custom segmentation heads for different segmentation tasks
-        self.cellprob_head = DeepSegmentationHead(
-            in_channels=decoder_channels[-1], out_channels=1
-        )
-        self.gradflow_head = DeepSegmentationHead(
-            in_channels=decoder_channels[-1], out_channels=2
-        )
-
-    def forward(self, x):
-        """Forward pass through the network"""
-        # Ensure the input shape is correct
-        self.check_input_shape(x)
-
-        # Encode the input and then decode it
-        features = self.encoder(x)
-        decoder_output = self.decoder(*features)
-
-        # Generate masks for cell probability and gradient flows
-        cellprob_mask = self.cellprob_head(decoder_output)
-        gradflow_mask = self.gradflow_head(decoder_output)
-
-        # Concatenate the masks for output
-        masks = torch.cat([gradflow_mask, cellprob_mask], dim=1)
-
-        return masks
-
-
-class DeepSegmentationHead(nn.Sequential):
-    """Custom segmentation head for generating specific masks"""
-
-    def __init__(
-        self, in_channels, out_channels, kernel_size=3, activation=None, upsampling=1
-    ):
-        # Define a sequence of layers for the segmentation head
-        layers = [
-            nn.Conv2d(
-                in_channels,
-                in_channels // 2,
-                kernel_size=kernel_size,
-                padding=kernel_size // 2,
-            ),
-            nn.Mish(inplace=True),
-            nn.BatchNorm2d(in_channels // 2),
-            nn.Conv2d(
-                in_channels // 2,
-                out_channels,
-                kernel_size=kernel_size,
-                padding=kernel_size // 2,
-            ),
-            nn.UpsamplingBilinear2d(scale_factor=upsampling)
-            if upsampling > 1
-            else nn.Identity(),
-            Activation(activation) if activation else nn.Identity(),
-        ]
-        super().__init__(*layers)
-
-
-def _convert_activations(module, from_activation, to_activation):
-    """Recursively convert activation functions in a module"""
-    for name, child in module.named_children():
-        if isinstance(child, from_activation):
-            setattr(module, name, to_activation)
-        else:
-            _convert_activations(child, from_activation, to_activation)

spacr/resources/MEDIAR/train_tools/models/__init__.py

@@ -1 +0,0 @@
-from .MEDIARFormer import *

spacr/resources/MEDIAR/train_tools/utils.py

@@ -1,70 +0,0 @@
-import torch
-import numpy as np
-import os, json, random
-from pprint import pprint
-
-__all__ = ["ConfLoader", "directory_setter", "random_seeder", "pprint_config"]
-
-
-class ConfLoader:
-    """
-    Load json config file using DictWithAttributeAccess object_hook.
-    ConfLoader(conf_name).opt attribute is the result of loading json config file.
-    """
-
-    class DictWithAttributeAccess(dict):
-        """
-        This inner class makes dict to be accessed same as class attribute.
-        For example, you can use opt.key instead of the opt['key'].
-        """
-
-        def __getattr__(self, key):
-            return self[key]
-
-        def __setattr__(self, key, value):
-            self[key] = value
-
-    def __init__(self, conf_name):
-        self.conf_name = conf_name
-        self.opt = self.__get_opt()
-
-    def __load_conf(self):
-        with open(self.conf_name, "r") as conf:
-            opt = json.load(
-                conf, object_hook=lambda dict: self.DictWithAttributeAccess(dict)
-            )
-        return opt
-
-    def __get_opt(self):
-        opt = self.__load_conf()
-        opt = self.DictWithAttributeAccess(opt)
-
-        return opt
-
-
-def directory_setter(path="./results", make_dir=False):
-    """
-    Make dictionary if not exists.
-    """
-    if not os.path.exists(path) and make_dir:
-        os.makedirs(path)  # make dir if not exist
-        print("directory %s is created" % path)
-
-    if not os.path.isdir(path):
-        raise NotADirectoryError(
-            "%s is not valid. set make_dir=True to make dir." % path
-        )
-
-
-def random_seeder(seed):
-    """Fix randomness."""
-    torch.manual_seed(seed)
-    np.random.seed(seed)
-    random.seed(seed)
-    torch.backends.cudnn.deterministic = True
-    torch.backends.cudnn.benchmark = False
-
-def pprint_config(opt):
-    print("\n" + "=" * 50 + " Configuration " + "=" * 50)
-    pprint(opt, compact=True)
-    print("=" * 115 + "\n")

spacr-0.5.0.dist-info/RECORD

@@ -1,190 +0,0 @@
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