celldetective 1.4.2__py3-none-any.whl → 1.5.0b0__py3-none-any.whl

celldetective/utils/downloaders.py

@@ -0,0 +1,197 @@
+import json
+import os
+import shutil
+import tempfile
+import zipfile
+from glob import glob
+from urllib.request import urlopen
+
+import numpy as np
+from tqdm import tqdm
+
+from celldetective.utils.io import remove_file_if_exists
+from celldetective import get_logger
+
+logger = get_logger()
+
+
+def get_zenodo_files(cat=None):
+
+    zenodo_json = os.sep.join(
+        [
+            os.path.split(os.path.dirname(os.path.realpath(__file__)))[0],
+            # "celldetective",
+            "links",
+            "zenodo.json",
+        ]
+    )
+    with open(zenodo_json, "r") as f:
+        zenodo_json = json.load(f)
+    all_files = list(zenodo_json["files"]["entries"].keys())
+    all_files_short = [f.replace(".zip", "") for f in all_files]
+
+    categories = []
+    for f in all_files_short:
+        if f.startswith("CP") or f.startswith("SD"):
+            category = os.sep.join(["models", "segmentation_generic"])
+        elif f.startswith("MCF7") or f.startswith("mcf7"):
+            category = os.sep.join(["models", "segmentation_targets"])
+        elif f.startswith("primNK") or f.startswith("lymphocytes"):
+            category = os.sep.join(["models", "segmentation_effectors"])
+        elif f.startswith("demo"):
+            category = "demos"
+        elif f.startswith("db-si"):
+            category = os.sep.join(["datasets", "signal_annotations"])
+        elif f.startswith("db"):
+            category = os.sep.join(["datasets", "segmentation_annotations"])
+        else:
+            category = os.sep.join(["models", "signal_detection"])
+        categories.append(category)
+
+    if cat is not None:
+        if cat in [
+            os.sep.join(["models", "segmentation_generic"]),
+            os.sep.join(["models", "segmentation_targets"]),
+            os.sep.join(["models", "segmentation_effectors"]),
+            "demos",
+            os.sep.join(["datasets", "signal_annotations"]),
+            os.sep.join(["datasets", "segmentation_annotations"]),
+            os.sep.join(["models", "signal_detection"]),
+        ]:
+            categories = np.array(categories)
+            all_files_short = np.array(all_files_short)
+            return list(all_files_short[np.where(categories == cat)[0]])
+        else:
+            return []
+    else:
+        return all_files_short, categories
+
+
+def download_url_to_file(url, dst, progress=True):
+    r"""Download object at the given URL to a local path.
+                    Thanks to torch, slightly modified, from Cellpose
+    Args:
+            url (string): URL of the object to download
+            dst (string): Full path where object will be saved, e.g. `/tmp/temporary_file`
+            progress (bool, optional): whether to display a progress bar to stderr
+                    Default: True
+
+    """
+    file_size = None
+    import ssl
+
+    ssl._create_default_https_context = ssl._create_unverified_context
+    u = urlopen(url)
+    meta = u.info()
+    if hasattr(meta, "getheaders"):
+        content_length = meta.getheaders("Content-Length")
+    else:
+        content_length = meta.get_all("Content-Length")
+    if content_length is not None and len(content_length) > 0:
+        file_size = int(content_length[0])
+    # We deliberately save it in a temp file and move it after
+    dst = os.path.expanduser(dst)
+    dst_dir = os.path.dirname(dst)
+    f = tempfile.NamedTemporaryFile(delete=False, dir=dst_dir)
+
+    # GUI Check
+    try:
+        from PyQt5.QtWidgets import QApplication, QProgressDialog
+        from PyQt5.QtCore import Qt
+
+        app = QApplication.instance()
+        use_gui = app is not None
+    except ImportError:
+        use_gui = False
+
+    try:
+        if use_gui and progress:
+            # Setup QProgressDialog
+            pd = QProgressDialog("Downloading...", "Cancel", 0, 100)
+            pd.setWindowTitle("Downloading content")
+            pd.setWindowModality(Qt.WindowModal)
+            pd.setMinimumDuration(0)
+            pd.setValue(0)
+
+            downloaded = 0
+            while True:
+                buffer = u.read(8192)
+                if len(buffer) == 0:
+                    break
+                f.write(buffer)
+                downloaded += len(buffer)
+                if file_size:
+                    perc = int(downloaded * 100 / file_size)
+                    pd.setValue(perc)
+                    pd.setLabelText(
+                        f"Downloading... {downloaded/1024/1024:.1f}/{file_size/1024/1024:.1f} MB"
+                    )
+
+                QApplication.processEvents()
+                if pd.wasCanceled():
+                    print("Download cancelled by user.")
+                    break
+            pd.close()
+
+        else:
+            # Console / TQDM fallback
+            with tqdm(
+                total=file_size,
+                disable=not progress,
+                unit="B",
+                unit_scale=True,
+                unit_divisor=1024,
+            ) as pbar:
+                while True:
+                    buffer = u.read(8192)  # 8192
+                    if len(buffer) == 0:
+                        break
+                    f.write(buffer)
+                    pbar.update(len(buffer))
+
+        f.close()
+        shutil.move(f.name, dst)
+    finally:
+        f.close()
+        remove_file_if_exists(f.name)
+
+
+def download_zenodo_file(file, output_dir):
+
+    logger.info(f"{file=} {output_dir=}")
+    zenodo_json = os.sep.join(
+        [
+            os.path.split(os.path.dirname(os.path.realpath(__file__)))[0],
+            # "celldetective",
+            "links",
+            "zenodo.json",
+        ]
+    )
+    logger.info(f"{zenodo_json=}")
+    with open(zenodo_json, "r") as f:
+        zenodo_json = json.load(f)
+    all_files = list(zenodo_json["files"]["entries"].keys())
+    all_files_short = [f.replace(".zip", "") for f in all_files]
+    zenodo_url = zenodo_json["links"]["files"].replace("api/", "")
+    full_links = ["/".join([zenodo_url, f]) for f in all_files]
+    index = all_files_short.index(file)
+    zip_url = full_links[index]
+
+    path_to_zip_file = os.sep.join([output_dir, "temp.zip"])
+    download_url_to_file(rf"{zip_url}", path_to_zip_file)
+    with zipfile.ZipFile(path_to_zip_file, "r") as zip_ref:
+        zip_ref.extractall(output_dir)
+
+    file_to_rename = glob(
+        os.sep.join(
+            [output_dir, file, "*[!.json][!.png][!.h5][!.csv][!.npy][!.tif][!.ini]"]
+        )
+    )
+    if (
+        len(file_to_rename) > 0
+        and not file_to_rename[0].endswith(os.sep)
+        and not file.startswith("demo")
+    ):
+        os.rename(file_to_rename[0], os.sep.join([output_dir, file, file]))
+
+    os.remove(path_to_zip_file)

celldetective/utils/event_detection/__init__.py

@@ -0,0 +1,8 @@
+from celldetective.signals import SignalDetectionModel
+from celldetective.utils.model_loaders import locate_signal_model
+
+def _prep_event_detection_model(model_name=None, use_gpu=True):
+    model_path = locate_signal_model(model_name)
+    signal_model = SignalDetectionModel(pretrained=model_path)
+    return signal_model
+