dsa-helpers 0.4.dev5__tar.gz → 0.5.dev0__tar.gz

dsa_helpers-0.5.dev0/.gitignore

@@ -0,0 +1,11 @@
+# Python environment directories.
+env/
+pyenv/
+
+*.pyc
+*.egg-info
+dist/
+.env
+
+# Ignore data directory created for testing the package.
+tests/data/

{dsa_helpers-0.4.dev5/dsa_helpers.egg-info → dsa_helpers-0.5.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dsa_helpers
-Version: 0.4.dev5
+Version: 0.5.dev0
 Summary: Utility functions for working with the DSA girder client.
 Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
 Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>

dsa_helpers-0.5.dev0/dsa_helpers/__init__.py

@@ -0,0 +1,16 @@
+# Shadow imports.
+from .imread import imread
+from .imwrite import imwrite
+from . import girder_utils, image_utils, dash, ml, mongo_utils, utils
+
+# Modules that should be available.
+__all__ = [
+    "girder_utils",
+    "image_utils",
+    "dash",
+    "ml",
+    "imread",
+    "imwrite",
+    "mongo_utils",
+    "utils",
+]

dsa_helpers-0.5.dev0/dsa_helpers/dash/__init__.py

@@ -0,0 +1,3 @@
+from . import header
+
+__all__ = ["dash_paperdragon_utils", "header_callbacks", "header"]

dsa_helpers-0.5.dev0/dsa_helpers/dash/dash_paperdragon_utils.py

@@ -0,0 +1,76 @@
+def format_ann_docs_for_paperjs(
+    geojson_ann_docs: list[dict], return_as_input_to_paper: bool = False
+) -> list[dict]:
+    """Format DSA annotations in the geojson format into a format that paperdragon
+    can read and show as polygons.
+
+    Args:
+        geojson_ann_docs (list[dict]): A list of geojson annotation documents.
+        return_as_input_to_paper (bool): Whether to return the formatted documents as
+            input to paper. Defaults to False.
+
+    Returns:
+        list[dict]: A list of formatted annotation documents for paperjs. Note that
+            it will return an empty list if the documents could not be formatted.
+
+    """
+    # NOTE: hard-coded to only do the first doc.
+    formatted_docs = []
+
+    # Loop through each annotation document.
+    for ann_doc in geojson_ann_docs:
+        # Grab the features of this document, contains the polygon info.
+        features_to_include = []
+
+        for feature in ann_doc["features"]:
+            geometry = feature["geometry"]
+            if geometry["type"] == "Polygon":
+                properties = feature["properties"]
+                properties["rescale"] = {"strokeWidth": properties["lineWidth"]}
+                properties["strokeColor"] = properties["lineColor"]
+                properties["source"] = "dsa"
+
+                # Paperjs only supports multipolygons.
+                geometry["type"] = "MultiPolygon"
+
+                coordinates = geometry["coordinates"]
+
+                adjusted_coordinates = [
+                    [[[int(coord) for coord in point[:2]] for point in coordinates[0]]]
+                ]
+
+                geometry["coordinates"] = adjusted_coordinates
+
+                features_to_include.append(feature)
+
+        if len(features_to_include):
+            formatted_docs.append(features_to_include)
+
+    if return_as_input_to_paper:
+        return get_input_to_paper_dict(formatted_docs)
+
+    return formatted_docs
+
+
+def get_input_to_paper_dict(formatted_docs: list[dict] | None = None) -> dict:
+    """Get the input to paper dictionary.
+
+    Args:
+        formatted_docs (list[dict]): A list of formatted annotation documents for paperjs.
+
+    Returns:
+        dict: The input to paper dictionary.
+
+    """
+    input_to_paper = [{"type": "clearItems"}]
+
+    if formatted_docs is not None and len(formatted_docs):
+        for doc in formatted_docs:
+            input_to_paper.append(
+                {
+                    "type": "drawItems",
+                    "itemList": doc,
+                }
+            )
+
+    return {"actions": input_to_paper}

{dsa_helpers-0.4.dev5 → dsa_helpers-0.5.dev0}/dsa_helpers/image_utils.py

@@ -13,6 +13,7 @@ def tile_image(
     stride: int | None = None,
     fill: int | tuple = (255, 255, 255),
     prepend_name: str = "",
+    overwrite: bool = False,
 ) -> pd.DataFrame:
     """Tile an image into smaller images.
 
@@ -25,6 +26,8 @@ def tile_image(
         fill (int | tuple, optional): The fill value for tiles over the edges.
             Defaults to (255, 255, 255).
         prepend_name (str, optional): A string to prepend to the tile names.
+        overwrite (bool, optional): Whether to overwrite existing images.
+            Defaults to False.
 
     Returns:
         pandas.DataFrame: A DataFrame with the tile locations.
@@ -38,9 +41,7 @@ def tile_image(
 
     # Pad the image to avoid tiles not of the right size.
     save_loc = Path(save_loc)
-
-    if not save_loc.exists():
-        save_loc.mkdir(parents=True)
+    save_loc.mkdir(parents=True, exist_ok=True)
 
     if stride is None:
         stride = tile_size
@@ -50,16 +51,18 @@ def tile_image(
     xys = [(x, y) for x in range(0, w, stride) for y in range(0, h, stride)]
 
     for xy in xys:
+        # Get the top left and bottom right coordinates of the tile.
         x, y = xy
-        # Get the tile from the image.
-        tile_img = img[x : x + tile_size, y : y + tile_size]
 
-        save_fp = str(save_loc.joinpath(f"{prepend_name}x-{x}y-{y}.png"))
+        # Filepath for saving tile.
+        save_fp = save_loc / f"{prepend_name}_x{x}y{y}tilesize{tile_size}.png"
 
-        imwrite(save_fp, tile_img)
+        if not save_fp.is_file() or overwrite:
+            # Get the tile from the image.
+            tile_img = img[y : y + tile_size, x : x + tile_size]
 
-        df_data.append([save_fp, x, y])
+            imwrite(save_fp, tile_img)
 
-    df = pd.DataFrame(df_data, columns=["fp", "x", "y"])
+        df_data.append([save_fp, x, y, tile_size])
 
-    return df
+    return pd.DataFrame(df_data, columns=["fp", "x", "y", "tile_size"])

{dsa_helpers-0.4.dev5 → dsa_helpers-0.5.dev0}/dsa_helpers/ml/metrics/binary_dice_coefficient_metric.py

@@ -7,7 +7,8 @@ def binary_dice_coefficient_metric(eval_pred):
     with torch.no_grad():
         logits, labels = eval_pred  # assumed both are numpy
 
-        logits_tensor = torch.from_numpy(logits)
+        logits_tensor = torch.from_numpy(logits).cpu()
+        labels_tensor = torch.from_numpy(labels).cpu()
 
         # Scale the logits to the size of the label.
         logits_tensor = nn.functional.interpolate(
@@ -17,6 +18,7 @@ def binary_dice_coefficient_metric(eval_pred):
             align_corners=False,
         ).argmax(dim=1)
 
-        pred_labels = logits_tensor.detach().cpu().numpy()
+        pred_labels = logits_tensor.detach().numpy()
+        labels = labels_tensor.numpy()
 
         return {"dice_coefficient": binary_dice_coefficient(pred_labels, labels)}

{dsa_helpers-0.4.dev5 → dsa_helpers-0.5.dev0}/dsa_helpers/ml/object_detection/__init__.py

@@ -2,4 +2,4 @@
 from .get_pearce_roi_images import get_pearce_roi_images
 from .tile_image import tile_image
 
-__all__ = ["utils"]
+__all__ = ["utils", "get_pearce_roi_images", "tile_image"]

{dsa_helpers-0.4.dev5 → dsa_helpers-0.5.dev0/dsa_helpers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dsa_helpers
-Version: 0.4.dev5
+Version: 0.5.dev0
 Summary: Utility functions for working with the DSA girder client.
 Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
 Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>

{dsa_helpers-0.4.dev5 → dsa_helpers-0.5.dev0}/dsa_helpers.egg-info/SOURCES.txt

@@ -9,7 +9,6 @@ dsa_helpers/girder_utils.py
 dsa_helpers/image_utils.py
 dsa_helpers/imread.py
 dsa_helpers/imwrite.py
-dsa_helpers/login.py
 dsa_helpers/mongo_utils.py
 dsa_helpers/utils.py
 dsa_helpers.egg-info/PKG-INFO
@@ -18,6 +17,7 @@ dsa_helpers.egg-info/dependency_links.txt
 dsa_helpers.egg-info/requires.txt
 dsa_helpers.egg-info/top_level.txt
 dsa_helpers/dash/__init__.py
+dsa_helpers/dash/dash_paperdragon_utils.py
 dsa_helpers/dash/header.py
 dsa_helpers/dash/header_callbacks.py
 dsa_helpers/ml/__init__.py

{dsa_helpers-0.4.dev5 → dsa_helpers-0.5.dev0}/pyproject.toml

@@ -35,7 +35,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
 ]
 keywords = ["dsa", "girder", "girder_client"]
-version = "v0.4dev5"
+version = "v0.5dev0"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"

{dsa_helpers-0.4.dev5 → dsa_helpers-0.5.dev0}/requirements.txt

@@ -1,3 +1,7 @@
+# For developing the package locally.
+build
+twine
+
 girder-client
 numpy
 setuptools

dsa_helpers-0.4.dev5/.gitignore

@@ -1,11 +0,0 @@
-# Python environment directories.
-env/
-pyenv/
-
-# Do not push the version file.
-dsa_utils/_version.py
-
-*.pyc
-*.egg-info
-dist/
-.env

dsa_helpers-0.4.dev5/dsa_helpers/__init__.py

@@ -1,8 +0,0 @@
-# Shadow imports.
-from .imread import imread
-from .imwrite import imwrite
-
-# Modules that should be available.
-# from . import girder_utils, image_utils, dash
-
-__all__ = ["girder_utils", "image_utils", "dash", "ml"]

dsa_helpers-0.4.dev5/dsa_helpers/dash/__init__.py

@@ -1 +0,0 @@
-from . import header

dsa_helpers-0.4.dev5/dsa_helpers/login.py

@@ -1,36 +0,0 @@
-# Login / authenticate function for the girder client.
-from girder_client import GirderClient
-
-
-def login(
-    api_url: str,
-    login_or_email: str | None = None,
-    password: str | None = None,
-    api_key: str | None = None,
-) -> GirderClient:
-    """Authenticate a girder client with the given credentials or interactively
-    if none is given.
-
-    Args:
-        api_url (str): The DSA girder API url.
-        login_or_email (str | None): The login or email. Defaults to None.
-        password (str | None): Password for login / email. Defaults to None.
-        api_key (str | None): The api key to authenticate with. Defaults to None.
-
-    Returns:
-        girder_client.GirderClient: The authenticated girder client.
-
-    """
-    gc = GirderClient(apiUrl=api_url)
-
-    if api_key is None:
-        if login_or_email is None:
-            _ = gc.authenticate(interactive=True)
-        elif password is None:
-            _ = gc.authenticate(username=login_or_email, interactive=True)
-        else:
-            _ = gc.authenticate(username=login_or_email, password=password)
-    else:
-        _ = gc.authenticate(apiKey=api_key)
-
-    return gc