🚨 DEV: Use logger Instead Of print (slide_info.py)

tests/test_exceptions.py

@@ -2,20 +2,12 @@
 
 import pytest
 
-from tiatoolbox import utils
 from tiatoolbox.tools.stainnorm import get_normalizer
-from tiatoolbox.utils.exceptions import FileNotSupported, MethodNotSupported
-from tiatoolbox.wsicore.slide_info import slide_info
+from tiatoolbox.utils.exceptions import MethodNotSupported
 
 
 def test_exception_tests():
     """Test for Exceptions."""
-    with pytest.raises(FileNotSupported):
-        utils.misc.save_yaml(
-            slide_info(input_path="/mnt/test/sample.txt", verbose=True).as_dict(),
-            "test.yaml",
-        )
-
     with pytest.raises(MethodNotSupported):
         get_normalizer(method_name="invalid_normalizer")
 

tests/test_slide_info.py

@@ -4,23 +4,7 @@
 
 from click.testing import CliRunner
 
-from tiatoolbox import cli, utils
-from tiatoolbox.wsicore.slide_info import slide_info
-
-
-def test_slide_info(sample_all_wsis, tmp_path):
-    """Test for slide_info as a python function."""
-    file_types = ("*.ndpi", "*.svs", "*.mrxs", "*.jp2")
-    files_all = utils.misc.grab_files_from_dir(
-        input_path=sample_all_wsis,
-        file_types=file_types,
-    )
-
-    for curr_file in files_all:
-        slide_param = slide_info(input_path=curr_file, verbose=True)
-        out_path = tmp_path / slide_param.file_path.with_suffix(".yaml").name
-        utils.misc.save_yaml(slide_param.as_dict(), out_path)
-
+from tiatoolbox import cli
 
 # -------------------------------------------------------------------------------------
 # Command Line Interface
@@ -42,6 +26,8 @@ def test_command_line_slide_info(sample_all_wsis, tmp_path):
             "*.ndpi, *.svs",
             "--output-path",
             str(tmp_path),
+            "--verbose",
+            "True",
         ],
     )
 
@@ -86,7 +72,7 @@ def test_command_line_slide_info_svs(sample_svs):
             "--mode",
             "show",
             "--verbose",
-            "False",
+            "True",
         ],
     )
 

tiatoolbox/cli/slide_info.py

@@ -1,6 +1,8 @@
 """Command line interface for slide_info."""
+import logging
 import pathlib
 
+from tiatoolbox import logger
 from tiatoolbox.cli.common import (
     cli_file_type,
     cli_img_input,
@@ -20,7 +22,7 @@
 )
 @cli_file_type(default="*.ndpi, *.svs, *.mrxs, *.jp2")
 @cli_mode(default="show")
-@cli_verbose(default=True)
+@cli_verbose(default=False)
 def slide_info(img_input, output_path, file_types, mode, verbose):
     """Displays or saves WSI metadata depending on the mode argument."""
     from tiatoolbox import utils, wsicore
@@ -30,16 +32,22 @@ def slide_info(img_input, output_path, file_types, mode, verbose):
     )
 
     for curr_file in files_all:
-        slide_param = wsicore.slide_info.slide_info(
-            input_path=curr_file, verbose=verbose or mode == "show"
-        )
+        curr_file = pathlib.Path(curr_file)
+        wsi = wsicore.wsireader.WSIReader.open(input_img=curr_file)
+
+        if verbose:
+            logger.setLevel(logging.DEBUG)
+            logger.debug(curr_file.name)
+
+        if mode == "show":
+            logger.info(wsi.info.as_dict())
 
         if mode == "save":
             out_path = pathlib.Path(
-                output_path, slide_param.file_path.with_suffix(".yaml").name
+                output_path, wsi.info.file_path.with_suffix(".yaml").name
             )
             utils.misc.save_yaml(
-                slide_param.as_dict(),
+                wsi.info.as_dict(),
                 out_path,
             )
-            print("Meta files saved at " + str(output_path))
+            logger.info("Meta files saved at %s.", str(output_path))

tiatoolbox/wsicore/__init__.py

@@ -1,2 +1,2 @@
 """Package to read whole slide images"""
-from tiatoolbox.wsicore import metadata, slide_info, wsimeta, wsireader
+from tiatoolbox.wsicore import metadata, wsimeta, wsireader