Merge pull request #11 from NxNiki/dev

NxNiki · web-flow · commit ebf6ab410123 · 2024-10-23T18:51:08.000-07:00
check how to lost whole sleep data.
diff --git a/scripts/plot_activation.ipynb b/scripts/plot_activation.ipynb
diff --git a/scripts/save_config.py b/scripts/save_config.py
@@ -6,57 +6,61 @@
 from brain_decoding.config.config import ExperimentConfig, PipelineConfig
 from brain_decoding.config.file_path import CONFIG_FILE_PATH, DATA_PATH, RESULT_PATH
 
-if __name__ == "__main__":
-    experiment_config = ExperimentConfig(name="sleep", patient=562)
+# if __name__ == "__main__":
+experiment_config = ExperimentConfig(name="sleep", patient=562)
 
-    config = PipelineConfig(experiment=experiment_config)
-    config.model.architecture = "multi-vit"
-    config.model.learning_rate = 1e-4
-    config.model.batch_size = 128
-    config.model.weight_decay = 1e-4
-    config.model.epochs = 40
-    config.model.lr_drop = 50
-    config.model.validation_step = 10
-    config.model.early_stop = 75
-    config.model.num_labels = 8
-    config.model.merge_label = True
-    config.model.img_embedding_size = 192
-    config.model.hidden_size = 256
-    config.model.num_hidden_layers = 6
-    config.model.num_attention_heads = 8
-    config.model.patch_size = (1, 5)
-    config.model.intermediate_size = 192 * 2
-    config.model.classifier_proj_size = 192
+config = PipelineConfig(experiment=experiment_config)
+config.model.architecture = "multi-vit"
+config.model.learning_rate = 1e-4
+config.model.batch_size = 128
+config.model.weight_decay = 1e-4
+config.model.epochs = 40
+config.model.lr_drop = 50
+config.model.validation_step = 10
+config.model.early_stop = 75
+config.model.num_labels = 8
+config.model.merge_label = True
+config.model.img_embedding_size = 192
+config.model.hidden_size = 256
+config.model.num_hidden_layers = 6
+config.model.num_attention_heads = 8
+config.model.patch_size = (1, 5)
+config.model.intermediate_size = 192 * 2
+config.model.classifier_proj_size = 192
 
-    config.experiment.seed = 42
-    config.experiment.use_spike = True
-    config.experiment.use_lfp = False
-    config.experiment.use_combined = False
-    config.experiment.use_shuffle = True
-    config.experiment.use_bipolar = False
-    config.experiment.use_sleep = (
-        True  # set true to use sleep data as inference dataset, otherwise use free recall, is this right?
-    )
-    config.experiment.use_overlap = False
-    config.experiment.use_long_input = False
-    config.experiment.use_spontaneous = False
-    config.experiment.use_augment = False
-    config.experiment.use_shuffle_diagnostic = True
-    config.experiment.testing_mode = True  # in testing mode, a maximum of 1e4 clusterless data will be loaded.
-    config.experiment.model_aggregate_type = "sum"
-    config.experiment.train_phase = ["movie_1"]
-    config.experiment.test_phase = ["sleep_2"]
+config.experiment.seed = 42
+config.experiment.use_spike = True
+config.experiment.use_lfp = False
+config.experiment.use_combined = False
+config.experiment.use_shuffle = True
+config.experiment.use_bipolar = False
+# config.experiment.use_sleep = (
+#     True  # set true to use sleep data as inference dataset, otherwise use free recall, is this right?
+# )
+config.experiment.use_overlap = False
+config.experiment.use_long_input = False
+config.experiment.use_spontaneous = False
+config.experiment.use_augment = False
+config.experiment.use_shuffle_diagnostic = True
+config.experiment.testing_mode = False  # in testing mode, a maximum of 1e4 clusterless data will be loaded.
+config.experiment.model_aggregate_type = "sum"
+config.experiment.train_phases = ["movie_1"]
+config.experiment.test_phases = ["sleep_2"]
+config.experiment.compute_accuracy = False
 
-    config.data.result_path = str(RESULT_PATH)
-    config.data.spike_path = str(DATA_PATH)
-    config.data.lfp_path = "undefined"
-    config.data.lfp_data_mode = "sf2000-bipolar-region-clean"
-    config.data.spike_data_mode = "notch CAR-quant-neg"
-    config.data.spike_data_mode_inference = "notch CAR-quant-neg"
-    config.data.spike_data_sd = [3.5]
-    config.data.spike_data_sd_inference = 3.5
-    config.data.model_aggregate_type = "sum"
-    config.data.movie_label_path = str(DATA_PATH / "8concepts_merged.npy")
-    config.data.movie_sampling_rate = 30
+config.experiment.ensure_list("train_phases")
+config.experiment.ensure_list("test_phases")
 
-    config.export_config(CONFIG_FILE_PATH)
+config.data.result_path = str(RESULT_PATH)
+config.data.spike_path = str(DATA_PATH)
+config.data.lfp_path = "undefined"
+config.data.lfp_data_mode = "sf2000-bipolar-region-clean"
+config.data.spike_data_mode = "notch CAR-quant-neg"
+config.data.spike_data_mode_inference = "notch CAR-quant-neg"
+config.data.spike_data_sd = [3.5]
+config.data.spike_data_sd_inference = 3.5
+config.data.model_aggregate_type = "sum"
+config.data.movie_label_path = str(DATA_PATH / "8concepts_merged.npy")
+config.data.movie_sampling_rate = 30
+
+# config.export_config(CONFIG_FILE_PATH)
diff --git a/src/brain_decoding/config/config.py b/src/brain_decoding/config/config.py
@@ -37,14 +37,19 @@ def __setattr__(self, name, value):
     def __contains__(self, key: str) -> bool:
         return hasattr(self, key)
 
+    def __repr__(self):
+        attrs = {k: v for k, v in self.__dict__.items() if not k.startswith("_")}
+        attr_str = "\n".join(f"    {key}: {value!r}" for key, value in attrs.items())
+        return f"{self.__class__.__name__}(\n{attr_str}\n)"
+
     def set_alias(self, name: str, alias: str) -> None:
         self.__dict__["_alias"][alias] = name
 
     def ensure_list(self, name: str):
+        """Mark the field to always be treated as a list"""
         value = getattr(self, name, None)
         if value is not None and not isinstance(value, list):
             setattr(self, name, [value])
-        # Mark the field to always be treated as a list
         self._list_fields.add(name)
 
 
@@ -112,8 +117,9 @@ def export_config(self, output_file: Union[str, Path] = "config.yaml") -> None:
         dir_path = output_file.parent
         dir_path.mkdir(parents=True, exist_ok=True)
 
+        config_data = self.model_dump()
         with open(output_file, "w") as file:
-            yaml.safe_dump(self.model_dump(), file)
+            yaml.safe_dump(config_data, file)
 
     @property
     def _file_tag(self) -> str:
diff --git a/src/brain_decoding/dataloader/save_clusterless.py b/src/brain_decoding/dataloader/save_clusterless.py
@@ -26,6 +26,8 @@
 
 from brain_decoding.config.file_path import DATA_PATH
 
+SECONDS_PER_HOUR = 3600
+
 OFFSET = {
     "555_1": 4.58,
     "562_1": 0,
@@ -115,8 +117,9 @@
 
 # is there a way to select the whole duration?
 SLEEP_TIME = {
-    "562_1": (0, 2 * 3600),  # memory test
-    "562_2": (0, 5 * 3600),  # memory test
+    "562_1": (0, 2 * SECONDS_PER_HOUR),  # memory test
+    "562_2": (0, 5 * SECONDS_PER_HOUR),  # memory test
+    "562_3": (0, 10 * SECONDS_PER_HOUR),  # memory test
 }
 
 CONTROL = {
@@ -820,7 +823,7 @@ def sort_filename(filename):
 if __name__ == "__main__":
     version = "notch CAR-quant-neg"
     SPIKE_ROOT_PATH = "/Users/XinNiuAdmin/Library/CloudStorage/Box-Box/Vwani_Movie/Clusterless/"
-    get_oneshot_clean("562", 2000, "Experiment6_MovieParadigm_notch", category="sleep", phase=2, version=version)
+    get_oneshot_clean("562", 2000, "Experiment6_MovieParadigm_notch", category="sleep", phase=3, version=version)
     # get_oneshot_clean("562", 2000, "presleep", category="movie", phase=1, version=version)
     # get_oneshot_clean("562", 2000, "presleep", category="recall", phase="FR1", version=version)
     # get_oneshot_clean("562", 2000, "postsleep", category="recall", phase="FR2", version=version)
diff --git a/src/brain_decoding/dataloader/test_data.py b/src/brain_decoding/dataloader/test_data.py
@@ -27,56 +27,23 @@ class InferenceDataset(Dataset):
     def __init__(self, config):
         self.config = config
         self.lfp_channel_by_region = {}
-        phases = config.data.phases
+
         spikes_data = None
         if self.config.experiment["use_spike"]:
             data_path = "spike_path"
-            if self.config.experiment["use_sleep"]:
-                config.experiment["spike_data_mode_inference"] = ""
-                spikes_data = self.read_recording_data(data_path, "time_sleep", phases[0])
-            else:
-                if (
-                    isinstance(self.config.experiment["free_recall_phase"], str)
-                    and "all" in self.config.experiment["free_recall_phase"]
-                ):
-                    for phase in phases:
-                        spikes_data = self.read_recording_data(data_path, "time_recall", phase)
-                elif (
-                    isinstance(self.config.experiment["free_recall_phase"], str)
-                    and "control" in self.config.experiment["free_recall_phase"]
-                ):
-                    spikes_data = self.read_recording_data(data_path, "time", None)
-                elif (
-                    isinstance(self.config.experiment["free_recall_phase"], str)
-                    and "movie" in self.config.experiment["free_recall_phase"]
-                ):
-                    spikes_data = self.read_recording_data(data_path, "time", None)
-                else:
-                    spikes_data = self.read_recording_data(data_path, "time_recall", None)
+            spikes_data = self.read_recording_data(data_path, "time", self.config.experiment.test_phases[0])
 
         lfp_data = None
         if self.config.experiment["use_lfp"]:
             data_path = "lfp_path"
-            if self.config.experiment.use_sleep:
-                config["spike_data_mode_inference"] = ""
-                lfp_data = self.read_recording_data(data_path, "spectrogram_sleep", "")
-            else:
-                if isinstance(self.config["free_recall_phase"], str) and "all" in self.config["free_recall_phase"]:
-                    for phase in phases:
-                        lfp_data = self.read_recording_data(data_path, "spectrogram_recall", phase)
-                elif (
-                    isinstance(self.config["free_recall_phase"], str) and "control" in self.config["free_recall_phase"]
-                ):
-                    lfp_data = self.read_recording_data(data_path, "spectrogram", None)
-                else:
-                    lfp_data = self.read_recording_data(data_path, "spectrogram_recall", None)
+            lfp_data = self.read_recording_data(data_path, "spectrogram_recall", self.config.experiment.test_phases[0])
             # self.lfp_data = {key: np.concatenate(value_list, axis=0) for key, value_list in self.lfp_data.items()}
 
         self.data = {"clusterless": spikes_data, "lfp": lfp_data}
         self.data_length = self.get_data_length()
         self.preprocess_data()
 
-    def read_recording_data(self, root_path: str, file_path_prefix: str, phase: Optional[str]) -> np.ndarray[float]:
+    def read_recording_data(self, root_path: str, file_path_prefix: str, phase: str) -> np.ndarray[float]:
         """
         read spike or lfp data.
 
@@ -85,10 +52,7 @@ def read_recording_data(self, root_path: str, file_path_prefix: str, phase: Opti
         :param phase:
         :return:
         """
-        if phase == "":
-            exp_file_path = file_path_prefix
-        else:
-            exp_file_path = f"{file_path_prefix}_{phase}"
+        exp_file_path = f"{file_path_prefix}_{phase}"
 
         recording_file_path = os.path.join(
             self.config.data[root_path],
@@ -100,7 +64,8 @@ def read_recording_data(self, root_path: str, file_path_prefix: str, phase: Opti
         recording_files = sorted(recording_files, key=sort_file_name)
 
         if not recording_files:
-            raise ValueError(f"not files found in: {recording_files}")
+            error_msg = f"not files found in: {recording_files}"
+            raise ValueError(error_msg)
 
         if root_path == "spike_path":
             data = self.load_clustless(recording_files)
diff --git a/src/brain_decoding/dataloader/train_data.py b/src/brain_decoding/dataloader/train_data.py
@@ -58,22 +58,13 @@ def __init__(self, config: PipelineConfig):
         self.smoothed_label = []
         self.lfp_channel_by_region = {}
 
-        if self.patient in ["564", "565"]:
-            categories = ["Movie_1", "Movie_2"]
-        else:
-            categories = ["Movie_1"]
-
-        if self.use_spontaneous:
-            categories.append("Control1")
-            categories.append("Control2")
-
         # create spike data
         if self.use_spike:
-            self.data["clusterless"] = self.load_data(config.data["spike_path"], categories)
+            self.data["clusterless"] = self.load_data(config.data["spike_path"], config.experiment.train_phases)
 
         # create lfp data
         if self.use_lfp:
-            self.data["lfp"] = self.load_data(config.data["lfp_path"], categories)
+            self.data["lfp"] = self.load_data(config.data["lfp_path"], config.experiment.train_phases)
 
         # for c, category in enumerate(categories):
         #     size = sample_size[c]
diff --git a/src/brain_decoding/main.py b/src/brain_decoding/main.py
@@ -17,6 +17,7 @@
 from brain_decoding.config.config import PipelineConfig
 from brain_decoding.config.file_path import CONFIG_FILE_PATH
 from brain_decoding.param.base_param import device
+from scripts.save_config import config
 
 # torch.autograd.set_detect_anomaly(True)
 # torch.backends.cuda.matmul.allow_tf32=True
@@ -28,17 +29,19 @@
 
 
 def set_config(
-    config_file: Union[str, Path],
+    config_file: Union[str, Path, PipelineConfig],
     patient_id: int,
-    phases: Union[List[str], str],
+    train_phases: Union[List[str], str],
+    test_phases: Union[List[str], str],
     spike_data_sd: Union[List[float], float, None] = None,
     spike_data_sd_inference: Optional[float] = None,
 ) -> PipelineConfig:
     """
     set parameters based on config file.
     :param config_file:
     :param patient_id:
-    :param phases:
+    :param train_phases:
+    :param test_phases:
     :param spike_data_sd:
     :param spike_data_sd_inference:
     :return:
@@ -47,15 +50,18 @@ def set_config(
     if isinstance(spike_data_sd, float):
         spike_data_sd = [spike_data_sd]
 
-    config = PipelineConfig.read_config(config_file)
+    if isinstance(config_file, PipelineConfig):
+        config = config_file
+    else:
+        config = PipelineConfig.read_config(config_file)
 
     config.experiment["patient"] = patient_id
     config.experiment.name = "8concepts"
 
-    if isinstance(phases, str):
-        config.data.phases = [phases]
-    else:
-        config.data.phases = phases
+    config.experiment.train_phases = [train_phases]
+
+    config.experiment.test_phases = test_phases
+    config.experiment.ensure_list("test_phases")
 
     if spike_data_sd is not None:
         config.data.spike_data_sd = spike_data_sd
@@ -110,13 +116,16 @@ def pipeline(config: PipelineConfig) -> Trainer:
 
 if __name__ == "__main__":
     patient = 562
-    phase = "2"
+    phase_train = "movie_1"
+    phase_test = "sleep_3"
     CONFIG_FILE = CONFIG_FILE_PATH / "config_sleep-None-None_2024-10-16-19:17:43.yaml"
 
     config = set_config(
-        CONFIG_FILE,
+        # CONFIG_FILE,
+        config,
         patient,
-        phase,
+        phase_train,
+        phase_test,
     )
 
     print("start: ", patient)
diff --git a/src/brain_decoding/trainer.py b/src/brain_decoding/trainer.py
@@ -144,8 +144,8 @@ def train(self, epochs, fold):
                 )
                 print()
                 print("WELCOME MEMORY TEST at: ", epoch)
-                stats_m = self.memory(epoch=epoch + 1, phase=self.config.data.phases[0], alongwith=[])
-                # self.memory(1, epoch=epoch+1, phase='all')
+                stats_m = self.memory(epoch=epoch + 1, phase=self.config.experiment.test_phases[0], alongwith=[])
+
                 if stats_m is not None:
                     overall_p = list(stats_m.values())
                     print("P: ", overall_p)
@@ -360,7 +360,7 @@ def memory(self, epoch=-1, phase: str = "free_recall1", alongwith=[]):
         torch.manual_seed(self.config.experiment["seed"])
         np.random.seed(self.config.experiment["seed"])
         random.seed(self.config.experiment["seed"])
-        self.config.experiment["free_recall_phase"] = phase
+        # self.config.experiment["test_phase"] = phase
         dataloaders = initialize_inference_dataloaders(self.config)
         model = initialize_model(self.config)
         # model = torch.compile(model)
@@ -448,7 +448,7 @@ def memory(self, epoch=-1, phase: str = "free_recall1", alongwith=[]):
         predictions = predictions[:, 0:8]
 
         # Perform Statistic Method
-        if not self.config.experiment["use_sleep"]:
+        if self.config.experiment["compute_accuracy"]:
             sts = Permutate(
                 config=self.config,
                 phase=phase,
diff --git a/src/brain_decoding/utils/initializer.py b/src/brain_decoding/utils/initializer.py
diff --git a/src/brain_decoding/utils/plot.py b/src/brain_decoding/utils/plot.py
