Implement WSI instantiation from URL; related to #1

README.md

@@ -1,11 +1,18 @@
 # LazySlide
 
+
+## Installation
+
+```bash
+pip install git+ssh://git@github.com/rendeirolab/LazySlide.git
+```
+
 ## Usage
 
 ```python
 import lazyslide as zs
 
-slide = ''  # Your SVS file
+slide = 'https://github.com/camicroscope/Distro/raw/master/images/sample.svs'  # Your SVS file
 wsi = zs.WSI(slide)
 wsi.plot_tissue()
 
@@ -21,10 +28,9 @@ wsi.plot_tissue(contours=True)
 
 wsi.create_tiles(tile_px=256, mpp=.5)
 wsi.plot_tissue(tiles=True)
-
 ```
 
-If you want to do feature extration
+To do feature extraction:
 ```python
 import torch
 from torch.utils.data import DataLoader
@@ -37,19 +43,18 @@ loader = DataLoader(
 resnet = torch.hub.load("pytorch/vision", "resnet50", weights="IMAGENET1K_V2")
 
 with torch.no_grad():
-    for tile in loader():
+    for tile in loader:
         tile_feature = resnet(tile)
-
 ```
 
 ### Developer Notes
 
-To make pyvips works on Windows:
+To make pyvips work on Windows:
 
 ```python
 import os
 vipsbin = ''
 os.environ['PATH'] = vipsbin + ';' + os.environ['PATH']
 
 import pyvips as vips
-```
+```

lazyslide/utils.py

@@ -1,6 +1,10 @@
+from pathlib import Path
 from dataclasses import dataclass, field
 from itertools import tee
 from typing import Type
+from urllib.parse import urlparse
+
+import requests
 
 from .readers.base import ReaderBase
 from .readers.vips import VipsReader
@@ -17,11 +21,7 @@ def pairwise(iterable):
 def get_reader(reader="auto") -> Type[ReaderBase]:
     """Return an available backend"""
 
-    readers = {
-        "openslide": None,
-        "vips": None,
-        "cucim": None
-    }
+    readers = {"openslide": None, "vips": None, "cucim": None}
 
     try:
         import openslide
@@ -53,6 +53,40 @@ def get_reader(reader="auto") -> Type[ReaderBase]:
         return readers[reader]
 
 
+def is_url(s: str) -> bool:
+    try:
+        result = urlparse(s)
+        return all([result.scheme, result.netloc])
+    except ValueError:
+        return False
+
+
+def download_file(url: str, file_path: Path, chunk_size: int = 1024):
+    """Download a file in chunks"""
+    r = requests.get(url, stream=True)
+    with file_path.open("wb") as fd:
+        for chunk in r.iter_content(chunk_size=chunk_size):
+            fd.write(chunk)
+
+
+def check_wsi_path(path: str | Path, allow_download: bool = True) -> Path:
+    import tempfile
+
+    # Check path is URL or Path
+    if isinstance(path, str):
+        if is_url(path):
+            if not allow_download:
+                raise ValueError("Given a URL but not allowed to download.")
+            file_path = Path(tempfile.mkdtemp()) / path.split("/")[-1].split("?")[0]
+            download_file(path, file_path)
+            return file_path
+        elif Path(path).exists():
+            return Path(path)
+    elif isinstance(path, Path):
+        if path.exists():
+            return path
+    raise ValueError("Path must be a URL or Path to existing file.")
+
 @dataclass
 class TileOps:
     level: int = 0

lazyslide/wsi.py

@@ -186,8 +186,9 @@ def get_split_image_indices(image_height, image_width, min_side=20000):
 
 
 class WSI:
+        from .utils import check_wsi_path
 
-    def __init__(self,
+        self.image = check_wsi_path(image)
                  image: Path | str,
                  h5_file: Path | str = None,
                  reader="auto",  # openslide, vips, cucim
@@ -220,6 +221,14 @@ def reader(self):
     def metadata(self):
         return self.reader.metadata
 
+    def move_wsi_file(self, new_path: Path) -> None:
+        new_path = Path(new_path)
+        if not new_path.exists():
+            self.image.rename(new_path)
+            self.image = new_path
+        else:
+            raise FileExistsError(f"File {new_path} already exists.")
+
     def create_mask(self, transform, name="user", level=-1, save=False):
         level = self.reader.translate_level(level)
         image = self.reader.get_level(level)