Merge pull request #34 from stevenhua0320/load-image-fix

Fix: fix loadimage function to robustly load image

Author: sbillinge

docs/examples/KFe2As2-00838.tif renamed to docs/examples/data/KFe2As2-00838.tif

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* `load_image()` function correctly finds files when passed a relative path.
+
+**Security:**
+
+* <news item>

news/load-image-fix.rst

@@ -16,6 +16,7 @@
 import fnmatch
 import os
 import time
+from pathlib import Path
 
 import numpy as np
 
@@ -24,14 +25,14 @@
 try:
     import fabio
 
-    def openImage(im):
+    def open_image(im):
         rv = fabio.openimage.openimage(im)
         return rv.data
 
 except ImportError:
     import tifffile
 
-    def openImage(im):
+    def open_image(im):
         rv = tifffile.imread(im)
         return rv
 
@@ -53,7 +54,7 @@ def __init__(self, p):
         self.config = p
         return
 
-    def flipImage(self, pic):
+    def flip_image(self, pic):
         """Flip image if configured in config.
 
         :param pic: 2d array, image array
@@ -65,32 +66,41 @@ def flipImage(self, pic):
             pic = np.array(pic[::-1, :])
         return pic
 
-    def loadImage(self, filename):
-        """Load image file, if failed (for example loading an incomplete
-        file), then it will keep trying loading file for 5s.
+    def load_image(self, filename):
+        """Load image file. If loading fails (e.g. incomplete file),
+        retry for 5 seconds (10×0.5s).
 
-        :param filename: str, image file name
-        :return: 2d ndarray, 2d image array (flipped)
+        :param filename: str or Path, image file name or path
+        :return: 2D ndarray, flipped image array
         """
-        if os.path.exists(filename):
+        filename = Path(
+            filename
+        ).expanduser()  # handle "~", make it a Path object
+        if filename.exists():
             filenamefull = filename
         else:
-            filenamefull = os.path.join(self.opendirectory, filename)
-        image = np.zeros(10000).reshape(100, 100)
-        if os.path.exists(filenamefull):
-            i = 0
-            while i < 10:
-                try:
-                    if os.path.splitext(filenamefull)[-1] == ".npy":
-                        image = np.load(filenamefull)
-                    else:
-                        image = openImage(filenamefull)
-                    i = 10
-                except FileNotFoundError:
-                    i = i + 1
-                    time.sleep(0.5)
-            image = self.flipImage(image)
-            image[image < 0] = 0
+            found_files = list(Path.home().rglob(filename.name))
+            filenamefull = found_files[0] if found_files else None
+
+        if filenamefull is None or not filenamefull.exists():
+            raise FileNotFoundError(
+                f"Error: file not found: {filename}, "
+                f"Please rerun specifying a valid filename."
+            )
+            return np.zeros((100, 100))
+
+        image = np.zeros((100, 100))
+        for _ in range(10):  # retry 10 times (5 seconds total)
+            try:
+                if filenamefull.suffix == ".npy":
+                    image = np.load(filenamefull)
+                else:
+                    image = open_image(filenamefull)
+                break
+            except FileNotFoundError:
+                time.sleep(0.5)
+        image = self.flip_image(image)
+        image[image < 0] = 0
         return image
 
     def genFileList(

src/diffpy/srxplanar/loadimage.py

@@ -155,7 +155,7 @@ def _getPic(self, image, flip=None, correction=None):
                 rv += self._getPic(imagefile)
             rv /= len(image)
         elif isinstance(image, str):
-            rv = self.loadimage.loadImage(image)
+            rv = self.loadimage.load_image(image)
             if correction is None or correction is True:
                 ce = self.config.cropedges
                 rv[ce[2] : -ce[3], ce[0] : -ce[1]] = (
@@ -165,7 +165,7 @@ def _getPic(self, image, flip=None, correction=None):
         else:
             rv = image
             if flip is True:
-                rv = self.loadimage.flipImage(rv)
+                rv = self.loadimage.flip_image(rv)
             if correction is True:
                 # rv *= self.correction
                 ce = self.config.cropedges
@@ -339,13 +339,13 @@ def createMask(self, filename=None, pic=None, addmask=None):
                     pic = self.pic
                 else:
                     pic = (
-                        self.loadimage.loadImage(filelist[0])
+                        self.loadimage.load_image(filelist[0])
                         if len(filelist) > 0
                         else None
                     )
             else:
                 pic = (
-                    self.loadimage.loadImage(filelist[0])
+                    self.loadimage.load_image(filelist[0])
                     if len(filelist) > 0
                     else None
                 )

src/diffpy/srxplanar/srxplanar.py

@@ -7,13 +7,22 @@
 @pytest.fixture
 def user_filesystem(tmp_path):
     base_dir = Path(tmp_path)
-    home_dir = base_dir / "home_dir"
-    home_dir.mkdir(parents=True, exist_ok=True)
     cwd_dir = base_dir / "cwd_dir"
-    cwd_dir.mkdir(parents=True, exist_ok=True)
+    home_dir = base_dir / "home_dir"
+    test_dir = base_dir / "test_dir"
+    for dir in (cwd_dir, home_dir, test_dir):
+        dir.mkdir(parents=True, exist_ok=True)
 
-    home_config_data = {"username": "home_username", "email": "home@email.com"}
+    home_config_data = {
+        "username": "home_username",
+        "email": "home@email.com",
+    }
     with open(home_dir / "diffpyconfig.json", "w") as f:
         json.dump(home_config_data, f)
 
-    yield tmp_path
+    yield {
+        "base": base_dir,
+        "cwd": cwd_dir,
+        "home": home_dir,
+        "test": test_dir,
+    }

tests/conftest.py

@@ -0,0 +1,66 @@
+import os
+import shutil
+from pathlib import Path
+from types import SimpleNamespace
+
+import pytest
+
+from diffpy.srxplanar.loadimage import LoadImage
+
+PROJECT_ROOT = Path(__file__).resolve().parents[1]
+
+load_image_param = [
+    # case 1: just filename of file in current directory.
+    # expect function loads tiff file from cwd
+    (["KFe2As2-00838.tif", False, False], [0, 26, 173]),
+    # case 2: absolute file path to file in another directory.
+    # expect file is found and correctly read.
+    (
+        ["home_dir/KFe2As2-00838.tif", True, False],
+        [102, 57, 136],
+    ),
+    # case 3: relative file path to file in another directory.
+    # expect file is found and correctly read
+    (["./KFe2As2-00838.tif", False, True], [39, 7, 0]),
+    # case 4: non-existent file that incurred by mistype.
+    (
+        ["nonexistent_file.tif", False, False],
+        FileNotFoundError,
+    ),
+    # case 5: relative file path to file in another directory.
+    # expect file to be flip both horizontally and vertically
+    # and correctly read
+    (["./KFe2As2-00838.tif", True, True], [0, 53, 21]),
+]
+
+
+@pytest.mark.parametrize("inputs, expected", load_image_param)
+def test_load_image(inputs, expected, user_filesystem):
+    home_dir = user_filesystem["home"]
+    cwd_dir = user_filesystem["cwd"]
+    os.chdir(cwd_dir)
+
+    expected_mean = 2595.7087
+    expected_shape = (2048, 2048)
+
+    # locate source example file inside project docs
+    source_file = (
+        PROJECT_ROOT / "docs" / "examples" / "data" / "KFe2As2-00838.tif"
+    )
+    shutil.copy(source_file, cwd_dir / "KFe2As2-00838.tif")
+    shutil.copy(source_file, home_dir / "KFe2As2-00838.tif")
+    config = SimpleNamespace(fliphorizontal=inputs[1], flipvertical=inputs[2])
+    try:
+        loader = LoadImage(config)
+        actual = loader.load_image(inputs[0])
+        assert actual.shape == expected_shape
+        assert actual.mean() == expected_mean
+        assert actual[1][0] == expected[0]
+        assert actual[1][1] == expected[1]
+        assert actual[2][5] == expected[2]
+    except FileNotFoundError:
+        pytest.raises(
+            FileNotFoundError,
+            match=r"file not found:"
+            r" .*Please rerun specifying a valid filename\.",
+        )