spacr 0.2.81__py3-none-any.whl → 0.3.1__py3-none-any.whl

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

@@ -0,0 +1,102 @@
+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

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

spacr/resources/MEDIAR/train_tools/utils.py

@@ -0,0 +1,70 @@
+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/settings.py

@@ -34,6 +34,7 @@ def set_default_settings_preprocess_generate_masks(src, settings={}):
     if 'src' not in settings:
         settings['src'] = 'path'
 
+    settings.setdefault('segmentation_mode', 'cellpose')
     settings.setdefault('preprocess', True)
     settings.setdefault('masks', True)
     settings.setdefault('save', True)
@@ -829,10 +830,11 @@ expected_types = {
     "custom_model_path":str,
     "generate_training_dataset":bool,
     'preload_batches':int,
+    "segmentation_mode":str,
     "train_DL_model":bool,
 }
 
-categories = {"General": ["src", "metadata_type", "custom_regex", "experiment", "channels", "magnification", "channel_dims", "apply_model_to_dataset", "generate_training_dataset", "train_DL_model"],
+categories = {"General": ["src", "metadata_type", "custom_regex", "experiment", "channels", "magnification", "channel_dims", "apply_model_to_dataset", "generate_training_dataset", "train_DL_model", "segmentation_mode"],
              "Cell": ["cell_intensity_range", "cell_size_range", "cell_chann_dim", "cell_channel", "cell_background", "cell_Signal_to_noise", "cell_CP_prob", "cell_FT", "remove_background_cell", "cell_min_size", "cell_mask_dim", "cytoplasm", "cytoplasm_min_size", "include_uninfected", "merge_edge_pathogen_cells", "adjust_cells"],
              "Nucleus": ["nucleus_intensity_range", "nucleus_size_range", "nucleus_chann_dim", "nucleus_channel", "nucleus_background", "nucleus_Signal_to_noise", "nucleus_CP_prob", "nucleus_FT", "remove_background_nucleus", "nucleus_min_size", "nucleus_mask_dim", "nucleus_loc"],
              "Pathogen": ["pathogen_intensity_range", "pathogen_size_range", "pathogen_chann_dim", "pathogen_channel", "pathogen_background", "pathogen_Signal_to_noise", "pathogen_CP_prob", "pathogen_FT", "pathogen_model", "remove_background_pathogen", "pathogen_min_size", "pathogen_mask_dim"],

spacr/utils.py

@@ -303,7 +303,10 @@ def _get_cellpose_batch_size():
     except Exception as e:
         return 8
 
-def _extract_filename_metadata(filenames, src, images_by_key, regular_expression, metadata_type='cellvoyager', pick_slice=False, skip_mode='01'):
+def _extract_filename_metadata(filenames, src, regular_expression, metadata_type='cellvoyager', pick_slice=False, skip_mode='01'):
+    
+    images_by_key = defaultdict(list)
+    
     for filename in filenames:
         match = regular_expression.match(filename)
         if match:
@@ -328,7 +331,6 @@ def _extract_filename_metadata(filenames, src, images_by_key, regular_expression
                 if metadata_type =='cq1':
                     orig_wellID = wellID
                     wellID = _convert_cq1_well_id(wellID)
-                    #clear_output(wait=True)
                     print(f'Converted Well ID: {orig_wellID} to {wellID}', end='\r', flush=True)
 
                 if pick_slice:
@@ -338,7 +340,7 @@ def _extract_filename_metadata(filenames, src, images_by_key, regular_expression
                         sliceid = '00'
 
                     if mode == skip_mode:
-                        continue      
+                        continue
                         
                 key = (plate, well, field, channel, mode)
                 with Image.open(os.path.join(src, filename)) as img:
@@ -1210,16 +1212,16 @@ def _calculate_recruitment(df, channel):
     for chan in channels:
         df[f'{object_type}_slope_channel_{chan}'] = 1
 
-    for chan in channels:
-        df[f'nucleus_coordinates_{chan}'] = df[[f'nucleus_channel_{chan}_centroid_weighted_local-0', f'nucleus_channel_{chan}_centroid_weighted_local-1']].values.tolist()
-        df[f'pathogen_coordinates_{chan}'] = df[[f'pathogen_channel_{chan}_centroid_weighted_local-0', f'pathogen_channel_{chan}_centroid_weighted_local-1']].values.tolist()
-        df[f'cell_coordinates_{chan}'] = df[[f'cell_channel_{chan}_centroid_weighted_local-0', f'cell_channel_{chan}_centroid_weighted_local-1']].values.tolist()
-        df[f'cytoplasm_coordinates_{chan}'] = df[[f'cytoplasm_channel_{chan}_centroid_weighted_local-0', f'cytoplasm_channel_{chan}_centroid_weighted_local-1']].values.tolist()
-
-        df[f'pathogen_cell_distance_channel_{chan}'] = df.apply(lambda row: np.sqrt((row[f'pathogen_coordinates_{chan}'][0] - row[f'cell_coordinates_{chan}'][0])**2 + 
-                                                      (row[f'pathogen_coordinates_{chan}'][1] - row[f'cell_coordinates_{chan}'][1])**2), axis=1)
-        df[f'nucleus_cell_distance_channel_{chan}'] = df.apply(lambda row: np.sqrt((row[f'nucleus_coordinates_{chan}'][0] - row[f'cell_coordinates_{chan}'][0])**2 + 
-                                                      (row[f'nucleus_coordinates_{chan}'][1] - row[f'cell_coordinates_{chan}'][1])**2), axis=1)
+    #for chan in channels:
+    #    df[f'nucleus_coordinates_{chan}'] = df[[f'nucleus_channel_{chan}_centroid_weighted_local-0', f'nucleus_channel_{chan}_centroid_weighted_local-1']].values.tolist()
+    #    df[f'pathogen_coordinates_{chan}'] = df[[f'pathogen_channel_{chan}_centroid_weighted_local-0', f'pathogen_channel_{chan}_centroid_weighted_local-1']].values.tolist()
+    #    df[f'cell_coordinates_{chan}'] = df[[f'cell_channel_{chan}_centroid_weighted_local-0', f'cell_channel_{chan}_centroid_weighted_local-1']].values.tolist()
+    #    df[f'cytoplasm_coordinates_{chan}'] = df[[f'cytoplasm_channel_{chan}_centroid_weighted_local-0', f'cytoplasm_channel_{chan}_centroid_weighted_local-1']].values.tolist()
+    # 
+    #    df[f'pathogen_cell_distance_channel_{chan}'] = df.apply(lambda row: np.sqrt((row[f'pathogen_coordinates_{chan}'][0] - row[f'cell_coordinates_{chan}'][0])**2 + 
+    #                                                  (row[f'pathogen_coordinates_{chan}'][1] - row[f'cell_coordinates_{chan}'][1])**2), axis=1)
+    #    df[f'nucleus_cell_distance_channel_{chan}'] = df.apply(lambda row: np.sqrt((row[f'nucleus_coordinates_{chan}'][0] - row[f'cell_coordinates_{chan}'][0])**2 + 
+    #                                                  (row[f'nucleus_coordinates_{chan}'][1] - row[f'cell_coordinates_{chan}'][1])**2), axis=1)
     return df
     
 def _group_by_well(df):

{spacr-0.2.81.dist-info → spacr-0.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.81
+Version: 0.3.1
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -50,6 +50,14 @@ Requires-Dist: rapidfuzz<4.0,>=3.9
 Requires-Dist: keyring<16.0,>=15.1
 Requires-Dist: screeninfo<1.0,>=0.8.1
 Requires-Dist: ipykernel
+Requires-Dist: gdown
+Requires-Dist: fastremap>=1.14.1
+Requires-Dist: monai>=1.3.0
+Requires-Dist: pytz>=2023.3.post1
+Requires-Dist: segmentation-models-pytorch>=0.3.3
+Requires-Dist: tifffile>=2023.4.12
+Requires-Dist: tqdm>=4.65.0
+Requires-Dist: wandb>=0.16.2
 Requires-Dist: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
 Requires-Dist: pytest<3.11,>=3.9; extra == "dev"

{spacr-0.2.81.dist-info → spacr-0.3.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-spacr/__init__.py,sha256=8NZIlJOY2OzRCFjXvqusFL7BfyEJwNqB2lL8QNB-Kgo,1141
+spacr/__init__.py,sha256=bKVlCCJatRBMqjfxSXds2D_Swjf30T6agvAQ0Usz80o,1176
 spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
 spacr/app_annotate.py,sha256=nEIL7Fle9CDKGo3sucG_03DgjUQt5W1M1IHBIpVBr08,2171
 spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
@@ -8,24 +8,78 @@ spacr/app_measure.py,sha256=_K7APYIeOKpV6e_LcqabBjvEi7mfq9Fch8175x1x0k8,162
 spacr/app_sequencing.py,sha256=DjG26jy4cpddnV8WOOAIiExtOe9MleVMY4MFa5uTo5w,157
 spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
 spacr/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
-spacr/core.py,sha256=B2KMyG6IrVtV9d4XQkXVblbvfFhgcMY2o-mtmqDVDic,146519
+spacr/core.py,sha256=uyZdJ93ysd8oXgRX9b-6iTCldJ0CM1dq5VxF-xbZyN8,150703
 spacr/deep_spacr.py,sha256=a2YewgkQvLV-95NYJAutnojvJmX4S8z_wv6Tb-XIgUI,34484
 spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
-spacr/gui.py,sha256=RMg0bgbUpO6JwaWuNVMwuVZ18j4WlER3nW0Eaa0YZ30,7883
-spacr/gui_core.py,sha256=gTgsBzhZ5Q4vl6fT8VwrHWZ6BXWW5FNli8CE3WNMfv0,39986
+spacr/gui.py,sha256=zUkIyAuOwwoMDoExxtI-QHRfOhE1R2rulXJDNxwSLGc,7947
+spacr/gui_core.py,sha256=ZUIqvK7x6NzgrmuTRbvwCTTSpU3yWUaId6MZjXv16us,40128
 spacr/gui_elements.py,sha256=OA514FUVRKAcdu9CFVOt7UEzn1vztakQ-rDyKqV0b9A,129771
-spacr/gui_utils.py,sha256=pq_bmZ527S1j2s6McvqMhHNI05hJycBhHM8GY_jH9Ng,30597
-spacr/io.py,sha256=ZtVNbEom8X8p_KfsuWw0glGwLg6S0CfwwevDPGdfiSc,117342
+spacr/gui_utils.py,sha256=DCI--DNoYDWY1q0Aohd0XwFqjdPM3K5kCgRKiJGTnfc,30697
+spacr/io.py,sha256=VjH_1zXmf0yEdtABnsoabCEIpU0S3wB-7Hog7_ntCdE,117267
 spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
-spacr/measure.py,sha256=4rmzH_a5Y0s1qALVi6YRut3xpnkJXs5vzeTPCEf3QS8,54871
-spacr/plot.py,sha256=xVnbML7WpAEzdJdrLeYRk6aPinZSiV2dLAeu4mh7n0k,73963
+spacr/measure.py,sha256=ooMOP2OE0BHUNqIkg0ltwV2FiO6hZDIcRC6A0YmGcws,54875
+spacr/mediar.py,sha256=5HaCyZYiOff74PCvHwKj-jSRua0QRoIv1mvElPfVKtY,14830
+spacr/plot.py,sha256=yFC5m54lB8xVnC7vQp50-FvRn6lCjCt2mgi2GeiRwSs,73979
 spacr/sequencing.py,sha256=92KmjFa8Ptwmpf-GtyH3-uX6djFOYR5lJjMBHeciqhs,66921
-spacr/settings.py,sha256=rxXvpbNSFL5GKluGCLu4sEsYg8oo8djtbnGXPJ5d8hc,67931
+spacr/settings.py,sha256=PfIPLyMyBAfOodtdgNT8QzbysNDxTnsONXdI-fKtIDQ,68038
 spacr/sim.py,sha256=FveaVgBi3eypO2oVB5Dx-v0CC1Ny7UPfXkJiiRRodAk,71212
 spacr/sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 spacr/timelapse.py,sha256=KMYCgHzf9LTZe-lWl5mvH2EjbKRE6OhpwdY13wEumGc,39504
-spacr/utils.py,sha256=OY65COsdaCFK04irC0L7tNPaOvI2x7PBIs9D9t-ToCg,189144
+spacr/utils.py,sha256=JGjL_Tg5ec1qmaf9BV3gqlREUpxjK8hutgPEGj5mAEs,189141
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
+spacr/resources/MEDIAR/.git,sha256=nHbNNUgehWnXyS2LbJZitX4kbpd1urzYgE0WZYvdMfc,53
+spacr/resources/MEDIAR/.gitignore,sha256=Ff1q9Nme14JUd-4Q3jZ65aeQ5X4uttptssVDgBVHYo8,152
+spacr/resources/MEDIAR/LICENSE,sha256=yEj_TRDLUfDpHDNM0StALXIt6mLqSgaV2hcCwa6_TcY,1065
+spacr/resources/MEDIAR/README.md,sha256=TlL2XhmmNhYTtaBlMCnlJRW-K7qOVeqH1ABLabZAe2k,11877
+spacr/resources/MEDIAR/SetupDict.py,sha256=oHyOrGgKTRYbTjqlLWv1HXWAQ39urXih9AI56h4vcFk,869
+spacr/resources/MEDIAR/evaluate.py,sha256=7exc1Du1RXGelme7wAodcqPd6VIe_nFdOoPT2w09O-4,2181
+spacr/resources/MEDIAR/generate_mapping.py,sha256=6FqWgAegWExUF2DFc_vOQzH1c7g9-efhNDpq2t7lGh8,3688
+spacr/resources/MEDIAR/main.py,sha256=8KKelA75anJbvpCGXQbAO5OipHE-hx-q04_OB2Z90NQ,3573
+spacr/resources/MEDIAR/predict.py,sha256=V2GUdy3LM595gCoAjBOk22-QitaKRKRqJX3Hgdc4FEU,2141
+spacr/resources/MEDIAR/requirements.txt,sha256=7fapaH6LrDiKsdkjkl8oQ8oR2u49-n-OChMWa5wg7fY,225
+spacr/resources/MEDIAR/config/baseline.json,sha256=moqZ8Bf0rf1hcoJswp9EvE1IrqSfO4lzJGkj3-emIqc,1603
+spacr/resources/MEDIAR/config/mediar_example.json,sha256=B6mFpDgCpOJpN4Foj1hC_X4zCRyWXra3XsZ0DBqvGnQ,2114
+spacr/resources/MEDIAR/config/pred/pred_mediar.json,sha256=oE4YmuPFfH6_rK9PFBRX18aIPalZfni3NYGfRtOhTIU,385
+spacr/resources/MEDIAR/config/step1_pretraining/phase1.json,sha256=UuIkrGMZZmfMYpreh41BH9Yq3fBhBxoWAyeOR53oGsU,1520
+spacr/resources/MEDIAR/config/step1_pretraining/phase2.json,sha256=CIoi54TOI74laouA222-iIBrRGTrZ3pg8HQolpDquxo,1640
+spacr/resources/MEDIAR/config/step2_finetuning/finetuning1.json,sha256=073AeKRJLv-O7gyET0_SAxnFkwZ-Rcc4zNoql3f1p7c,1923
+spacr/resources/MEDIAR/config/step2_finetuning/finetuning2.json,sha256=SfNAH5Kt3Xet23JN0CKp7Lnm8mKNpOYrdmQZ0BBM5Rs,1936
+spacr/resources/MEDIAR/config/step3_prediction/base_prediction.json,sha256=qCinHOIatRvgqhNF-Ucx6YwIj9lRVWj0p_O9z5OY6j8,478
+spacr/resources/MEDIAR/config/step3_prediction/ensemble_tta.json,sha256=7NmBQTgyGBw1XFB4uWEGebj8CAoh1FklJbJPuhQwQQg,803
+spacr/resources/MEDIAR/core/BasePredictor.py,sha256=lvjAnHK7WXoaqnWI-1juf3_XU_v-ePo8Rme6qJc7Uq4,3664
+spacr/resources/MEDIAR/core/BaseTrainer.py,sha256=E-fayADu9A5Vd80NyZY49xFl2lPgLsoh4Nd3HkDjp5U,7428
+spacr/resources/MEDIAR/core/__init__.py,sha256=pR63haYRlkWrc9btVLSLVhk6nc94vmqreAs5H8I9LOw,46
+spacr/resources/MEDIAR/core/utils.py,sha256=h4z0Mdl08p3ftOwfAqtMVJ9-c6qBVna_9w9s0L25YBM,948
+spacr/resources/MEDIAR/core/Baseline/Predictor.py,sha256=mDHSG2jSJyLWr_j2gSzADjfmb0Ol76GI30HfpV0XR3U,1535
+spacr/resources/MEDIAR/core/Baseline/Trainer.py,sha256=OzkFeSF0sRn1Wej253I4h99f7v9wD3tKv88YYXLAtd4,3451
+spacr/resources/MEDIAR/core/Baseline/__init__.py,sha256=WinVVW50c_UhZDcUkX4RESjy8eSQOjMiU-KynfSGP_I,48
+spacr/resources/MEDIAR/core/Baseline/utils.py,sha256=V2e4a00ZdYFlHFaorLTI1CgX8gt_KFSfrpm_XikygiA,2370
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