Provide more error feedback during image import in the GUI

docs/release/release_v1.5.md

@@ -75,6 +75,8 @@ See the [table of CLI changes](../cli.md#changes-in-magellanmapper-v15) for a su
     - Plane index is only added when exporting multiple planes
 - Improvements to image import
     - Single plane RAW images can be loaded when importing files from a directory, in addition to multiplane RAW files
+    - Skips single plane files that give errors (eg non-image files in the input directory)
+    - Provides import error feedback in the GUI
     - The known parts of the import image shape are populated even if the full shape is not known
     - The Bio-Formats library has been updated to support more file formats (from Bio-Formats 5.1.8 to 6.6.0 via Python-Bioformats 1.1.0 to 4.0.5, respectively)
     - Fixed to disable the import directory button when metadata is insufficient

magmap/gui/import_threads.py

@@ -6,6 +6,8 @@
 from magmap.io import importer
 from magmap.settings import config
 
+_logger = config.logger.getChild(__name__)
+
 
 class SetupImportThread(QtCore.QThread):
     """Thread for setting up file import by extracting image metadata.
@@ -81,6 +83,14 @@ def run(self):
                 img5d = importer.import_multiplane_images(
                     self.chl_paths, self.prefix, self.import_md, config.series,
                     fn_feedback=self.fn_feedback)
+
+        except Exception as e:
+            # provide feedback for any errors during import
+            self.fn_feedback(f"Error during import:\n{e}")
+            if config.log_path:
+                self.fn_feedback(f"See log for more info: {config.log_path}\n")
+            _logger.exception(e)
+
         finally:
             if img5d is not None:
                 # set up the image for immediate use within MagellanMapper

magmap/io/cli.py

@@ -413,7 +413,7 @@ def process_cli_args():
             log_path = os.path.join(
                 config.user_app_dirs.user_data_dir, "out.log")
         # log to file
-        logs.add_file_handler(config.logger, log_path)
+        config.log_path = logs.add_file_handler(config.logger, log_path)
 
     # redirect standard out/error to logging
     sys.stdout = logs.LogWriter(config.logger.info)

magmap/io/importer.py

@@ -1162,44 +1162,51 @@ def import_files():
         for filei, file in enumerate(chl_files):
             libmag.printcb("importing {}".format(file), fn_feedback)
             try:
-                # load standard image types
-                img = io.imread(file)
-            except ValueError:
-                # load as a RAW image file
-                img = np.memmap(
-                    file, dtype=import_md[config.MetaKeys.DTYPE],
-                    shape=tuple(import_md[config.MetaKeys.SHAPE][2:4]),
-                    mode="r")
-
-            if rgb_to_grayscale and img.ndim >= 3 and img.shape[2] == 3:
-                # assume that 3-channel images are RGB
-                # TODO: remove rgb_to_grayscale since must give single channel?
-                print("converted from 3-channel (assuming RGB) to grayscale")
-                img = color.rgb2gray(img)
-
-            if img5d is None:
-                # generate an array for all planes and channels based on
-                # dimensions of the first extracted plane and any channel keys
-                shape = [1, len(chl_files), *img.shape]
+                try:
+                    # load standard image types
+                    img = io.imread(file)
+                except ValueError:
+                    # load as a RAW image file
+                    img = np.memmap(
+                        file, dtype=import_md[config.MetaKeys.DTYPE],
+                        shape=tuple(import_md[config.MetaKeys.SHAPE][2:4]),
+                        mode="r")
+
+                if rgb_to_grayscale and img.ndim >= 3 and img.shape[2] == 3:
+                    # assume that 3-channel images are RGB
+                    # TODO: remove rgb_to_grayscale since must give single chl?
+                    libmag.printcb(
+                        "Converted from 3-channel (assuming RGB) to grayscale",
+                        fn_feedback)
+                    img = color.rgb2gray(img)
+
+                if img5d is None:
+                    # generate an array for all planes and channels based on
+                    # dims of the first extracted plane and any channel keys
+                    shape = [1, len(chl_files), *img.shape]
+                    if num_chls > 1:
+                        shape.append(num_chls)
+                    os.makedirs(
+                        os.path.dirname(filename_image5d_npz), exist_ok=True)
+                    img5d = np.lib.format.open_memmap(
+                        filename_image5d_npz, mode="w+", dtype=img.dtype,
+                        shape=tuple(shape))
+
+                # insert plane, without using channel dimension if no channel
+                # designators were found in file names
                 if num_chls > 1:
-                    shape.append(num_chls)
-                os.makedirs(
-                    os.path.dirname(filename_image5d_npz), exist_ok=True)
-                img5d = np.lib.format.open_memmap(
-                    filename_image5d_npz, mode="w+", dtype=img.dtype,
-                    shape=tuple(shape))
-
-            # insert plane, without using channel dimension if no channel
-            # designators were found in file names
-            if num_chls > 1:
-                img5d[0, filei, ..., chli] = img
-            else:
-                img5d[0, filei] = img
-
-            # measure near low/high intensity values
-            low, high = np.percentile(img, (0.5, 99.5))
-            lows.append(low)
-            highs.append(high)
+                    img5d[0, filei, ..., chli] = img
+                else:
+                    img5d[0, filei] = img
+
+                # measure near low/high intensity values
+                low, high = np.percentile(img, (0.5, 99.5))
+                lows.append(low)
+                highs.append(high)
+            except ValueError as e1:
+                libmag.printcb(
+                    f"Could not load '{file}'; skipping it because of error: "
+                    f"{e1}", fn_feedback)
 
         lows_chls.append(min(lows))
         highs_chls.append(max(highs))

magmap/settings/config.py

@@ -65,6 +65,9 @@ class Verbosity(Enum):
 #: :class:`logging.Logger`: Root logger for the application.
 logger = logs.setup_logger()
 
+#: Path to log file.
+log_path: Optional[pathlib.Path] = None
+
 
 # IMAGE FILES
 

magmap/settings/logs.py

@@ -98,7 +98,8 @@ def update_log_level(logger, level):
     return logger
 
 
-def add_file_handler(logger, path, backups=5):
+def add_file_handler(
+        logger: logging.Logger, path: str, backups: int = 5) -> pathlib.Path:
     """Add a rotating log file handler with a new log file.
 
     Rotates the file each time this function is called for the given number
@@ -107,17 +108,18 @@ def add_file_handler(logger, path, backups=5):
     creating a log filed named with an incremented number (eg ``out1.log``).
 
     Args:
-        logger (:class:`logging.Logger`): Logger to update.
-        path (str): Path to log. Increments to ``path<n>.<ext>`` if the
+        logger: Logger to update.
+        path: Path to log. Increments to ``path<n>.<ext>`` if the
             file at ``path`` cannot be rotated.
-        backups (int): Number of backups to maintain; defaults to 5.
+        backups: Number of backups to maintain; defaults to 5.
 
     Returns:
-        :class:`logging.Logger`: The logger for chained calls.
+        The log output path.
 
     """
     # check if log file already exists
     pathl = pathlib.Path(path)
+    path_log = pathl
     roll = pathl.is_file()
 
     # create a rotations file handler to manage number of backups while
@@ -129,8 +131,8 @@ def add_file_handler(logger, path, backups=5):
         try:
             # if the existing file at path cannot be rotated, increment the
             # filename to create a new series of rotating log files
-            path_log = (pathl if i == 0 else
-                        f"{pathl.parent / pathl.stem}{i}{pathl.suffix}")
+            path_log = pathl if i == 0 else pathlib.Path(
+                f"{pathl.parent / pathl.stem}{i}{pathl.suffix}")
             logger.debug(f"Trying logger path: {path_log}")
             handler_file = handlers.RotatingFileHandler(
                 path_log, backupCount=backups)
@@ -150,4 +152,4 @@ def add_file_handler(logger, path, backups=5):
         "%(asctime)s - %(name)s - %(levelname)s - %(message)s"))
     logger.addHandler(handler_file)
 
-    return logger
+    return path_log