Merge pull request #9 from Aharoni-Lab/bugfix-relative-paths

bugfix: relative and absolute paths

miniscope_io/io.py

@@ -29,15 +29,10 @@ class SDCard:
     def __init__(
             self,
             drive: Union[str, Path],
-            layout: SDLayout,
-            directpath: bool = False
+            layout: SDLayout
         ):
 
-        if directpath == False:
-            self.drive = Path(drive).resolve()
-        else:
-            self.drive = drive
-    # Logs the error appropriately. 
+        self.drive = drive
         self.layout = layout
 
         # Private attributes used when the file reading context is entered
@@ -72,20 +67,17 @@ def __init__(
     @property
     def config(self) -> SDConfig:
         if self._config is None:
-            try:
-                with open(self.drive, 'rb') as sd:
-                    sd.seek(self.layout.sectors.config_pos, 0)
-                    configSectorData = np.frombuffer(sd.read(self.layout.sectors.size), dtype=np.uint32)
-
-                self._config = SDConfig(
-                    **{
-                        k: configSectorData[v]
-                        for k, v in self.layout.config.dict().items()
-                        if v is not None
-                    }
-                )
-            except Exception as error:
-                print("An exception occurred:", error)
+            with open(self.drive, 'rb') as sd:
+                sd.seek(self.layout.sectors.config_pos, 0)
+                configSectorData = np.frombuffer(sd.read(self.layout.sectors.size), dtype=np.uint32)
+
+            self._config = SDConfig(
+                **{
+                    k: configSectorData[v]
+                    for k, v in self.layout.config.dict().items()
+                    if v is not None
+                }
+            )
 
         return self._config
 

tests/test_io.py

@@ -1,6 +1,10 @@
 import pytest
+from pathlib import Path
+import os
 
 from miniscope_io.sdcard import DataHeader
+from miniscope_io.formats import WireFreeSDLayout
+from miniscope_io.io import SDCard
 from miniscope_io.exceptions import EndOfRecordingException
 from miniscope_io.data import Frame
 
@@ -77,6 +81,31 @@ def test_frame_count(wirefree):
         with pytest.raises(EndOfRecordingException):
             frame = wirefree.read()
 
+def test_relative_path():
+    """
+    Test that we can use both relative and absolute paths in the SD card model
+    """
+    # get absolute path of working directory, then get relative path to data from there
+    abs_cwd = Path(os.getcwd()).resolve()
+    abs_child = Path(__file__).parent.parent / 'data' / 'wirefree_example.img'
+    rel_path = abs_child.relative_to(abs_cwd)
+
+    assert not rel_path.is_absolute()
+    sdcard = SDCard(drive = rel_path, layout = WireFreeSDLayout)
+
+    # check we can do something basic like read config
+    assert sdcard.config is not None
+
+    # check it remains relative after init
+    assert not sdcard.drive.is_absolute()
+
+    # now try with an absolute path
+    abs_path = rel_path.resolve()
+    assert abs_path.is_absolute()
+    sdcard_abs = SDCard(drive= abs_path, layout= WireFreeSDLayout)
+    assert sdcard_abs.config is not None
+    assert sdcard_abs.drive.is_absolute()
+
 
 #
 # @pytest.mark.parametrize(