Merge branch 'master' into neuralynx

zm711 · web-flow · commit 5155bd0cd4bd · 2025-04-07T08:19:14.000-04:00
diff --git a/neo/io/tiffio.py b/neo/io/tiffio.py
@@ -15,35 +15,53 @@ class TiffIO(BaseIO):
     """
     Neo IO module for optical imaging data stored as a folder of TIFF images.
 
-    *Usage*:
-        >>> from neo import io
-        >>> import quantities as pq
-        >>> r = io.TiffIO("dir_tiff",spatial_scale=1.0*pq.mm, units='V',
-        ...               sampling_rate=1.0*pq.Hz)
-        >>> block = r.read_block()
-        read block
-        creating segment
-        returning block
-        >>> block
-        Block with 1 segments
-        file_origin: 'test'
-        # segments (N=1)
-        0: Segment with 1 imagesequences
-            annotations: {'tiff_file_names': ['file_tif_1_.tiff',
-                'file_tif_2.tiff',
-                'file_tif_3.tiff',
-                'file_tif_4.tiff',
-                'file_tif_5.tiff',
-                'file_tif_6.tiff',
-                'file_tif_7.tiff',
-                'file_tif_8.tiff',
-                'file_tif_9.tiff',
-                'file_tif_10.tiff',
-                'file_tif_11.tiff',
-                'file_tif_12.tiff',
-                'file_tif_13.tiff',
-                'file_tif_14.tiff']}
-            # analogsignals (N=0)
+    Parameters
+    ----------
+    directory_path: Path | str | None, default: None
+        The path to the folder containing tiff images
+    units: Quantity units | None, default: None
+        the units for creating the ImageSequence
+    sampling_rate: Quantity Units | None, default: None
+        The sampling rate
+    spatial_scale: Quantity unit | None, default: None
+        The scale of the images
+    origin: Literal['top-left'| 'bottom-left'], default: 'top-left'
+        Whether to use the python default origin for images which is upper left corner ('top-left')
+        as orgin or to use a bottom left corner as orgin ('bottom-left')
+        Note that plotting functions like matplotlib.pyplot.imshow expect upper left corner.
+    **kwargs: dict
+        The standard neo annotation kwargs
+
+    Examples
+    --------
+    >>> from neo import io
+    >>> import quantities as pq
+    >>> r = io.TiffIO("dir_tiff",spatial_scale=1.0*pq.mm, units='V',
+    ...               sampling_rate=1.0*pq.Hz)
+    >>> block = r.read_block()
+    read block
+    creating segment
+    returning block
+    >>> block
+    Block with 1 segments
+    file_origin: 'test'
+    # segments (N=1)
+    0: Segment with 1 imagesequences
+        annotations: {'tiff_file_names': ['file_tif_1_.tiff',
+            'file_tif_2.tiff',
+            'file_tif_3.tiff',
+            'file_tif_4.tiff',
+            'file_tif_5.tiff',
+            'file_tif_6.tiff',
+            'file_tif_7.tiff',
+            'file_tif_8.tiff',
+            'file_tif_9.tiff',
+            'file_tif_10.tiff',
+            'file_tif_11.tiff',
+            'file_tif_12.tiff',
+            'file_tif_13.tiff',
+            'file_tif_14.tiff']}
+        # analogsignals (N=0)
     """
 
     name = "TIFF IO"
@@ -66,13 +84,30 @@ class TiffIO(BaseIO):
 
     mode = "dir"
 
-    def __init__(self, directory_path=None, units=None, sampling_rate=None, spatial_scale=None, **kwargs):
-        import PIL
+    def __init__(
+        self,
+        directory_path=None,
+        units=None,
+        sampling_rate=None,
+        spatial_scale=None,
+        origin="top-left",
+        **kwargs,
+    ):
+        # this block is because people might be confused about the PIL -> pillow change
+        # between python2 -> python3 (both with namespace PIL)
+        try:
+            import PIL
+        except ImportError:
+            raise ImportError("To use TiffIO you must first `pip install pillow`")
+
+        if origin != "top-left" and origin != "bottom-left":
+            raise ValueError("`origin` must be either `top-left` or `bottom-left`")
 
         BaseIO.__init__(self, directory_path, **kwargs)
         self.units = units
         self.sampling_rate = sampling_rate
         self.spatial_scale = spatial_scale
+        self.origin = origin
 
     def read_block(self, lazy=False, **kwargs):
         import PIL
@@ -98,13 +133,17 @@ def natural_sort(l):
         list_data_image = []
         for file_name in file_name_list:
             data = np.array(PIL.Image.open(self.filename + "/" + file_name)).astype(np.float32)
+            if self.origin == "bottom-left":
+                data = np.flip(data, axis=-2)
             list_data_image.append(data)
         list_data_image = np.array(list_data_image)
         if len(list_data_image.shape) == 4:
             list_data_image = []
             for file_name in file_name_list:
                 image = PIL.Image.open(self.filename + "/" + file_name).convert("L")
                 data = np.array(image).astype(np.float32)
+                if self.origin == "bottom-left":
+                    data = np.flip(data, axis=-2)
                 list_data_image.append(data)
 
         print("read block")
diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
@@ -566,7 +566,7 @@ def _demultiplex_digital_data(self, raw_digital_data, channel_ids, i_start, i_st
         set high and the rest low, the 16-bit word would be 2^0 + 2^4 + 2^5 = 1 + 16 + 32 = 49.
 
         The native_order property for each channel corresponds to its bit position in the packed word.
-        
+
         """
         dtype = np.uint16  # We fix this to match the memmap dtype
         output = np.zeros((i_stop - i_start, len(channel_ids)), dtype=dtype)
@@ -902,7 +902,7 @@ def read_rhs(filename, file_format: str):
 
         # Each DC amplifier channel has a corresponding RHS2000 amplifier channel
         channel_number_dict["DC Amplifier channel"] = channel_number_dict["RHS2000 amplifier channel"]
-        
+
         if file_format == "one-file-per-channel":
             # There is a way to shut off saving amplifier data and only keeping the DC amplifier or shutting off all amplifier file saving,
             # so we need to count the number of files we find instead of relying on the header.
@@ -913,7 +913,6 @@ def read_rhs(filename, file_format: str):
         else:
             channel_number_dict["Stim channel"] = channel_number_dict["RHS2000 amplifier channel"]
 
-
         header_size = f.tell()
 
     sr = global_info["sampling_rate"]
diff --git a/neo/test/iotest/test_intanio.py b/neo/test/iotest/test_intanio.py
@@ -23,9 +23,9 @@ class TestIntanIO(
         "intan/intan_fpc_rhs_test_240329_091637/info.rhs",  # Format one-file-per-channel
         "intan/intan_fps_rhs_test_240329_091536/info.rhs",  # Format one-file-per-signal
         "intan/rhd_fpc_multistim_240514_082044/info.rhd",  # Multiple digital channels one-file-per-channel rhd
-        "intan/rhs_stim_data_single_file_format/intanTestFile.rhs", # header-attached rhs data with stimulus current 
-        "intan/test_fcs_dc_250327_154333/info.rhs", # this is an example of only having dc amp rather than amp files
-        #"intan/test_fpc_stim_250327_151617/info.rhs", # wrong files Heberto will fix
+        "intan/rhs_stim_data_single_file_format/intanTestFile.rhs",  # header-attached rhs data with stimulus current
+        "intan/test_fcs_dc_250327_154333/info.rhs",  # this is an example of only having dc amp rather than amp files
+        # "intan/test_fpc_stim_250327_151617/info.rhs", # wrong files Heberto will fix
     ]
 
 
diff --git a/neo/test/iotest/test_tiffio.py b/neo/test/iotest/test_tiffio.py
@@ -17,13 +17,14 @@ def test_read_group_of_tiff_grayscale(self):
         img = []
         for picture in range(10):
             img.append([])
-            for y in range(50):
+            for x in range(50):
                 img[picture].append([])
-                for x in range(50):
-                    img[picture][y].append(x)
+                for y in range(50):
+                    img[picture][x].append(y)
         img = np.array(img, dtype=float)
         for image in range(10):
-            Image.fromarray(img[image]).save(directory + "/tiff_exemple" + str(image) + ".tif")
+            # rotate image by 90 deg so that shifting the origin is meaningful in later test
+            Image.fromarray(np.rot90(img[image])).save(directory + "/tiff_exemple" + str(image) + ".tif")
 
         ioclass = TiffIO(
             directory_path=directory, units="V", sampling_rate=1.0 * pq.Hz, spatial_scale=1.0 * pq.micrometer
@@ -35,6 +36,21 @@ def test_read_group_of_tiff_grayscale(self):
         self.assertEqual(blck.segments[0].imagesequences[0].sampling_rate, 1.0 * pq.Hz)
         self.assertEqual(blck.segments[0].imagesequences[0].spatial_scale, 1.0 * pq.micrometer)
 
+        ioclass_bl_origin = TiffIO(
+            directory_path=directory,
+            units="V",
+            sampling_rate=1.0 * pq.Hz,
+            spatial_scale=1.0 * pq.micrometer,
+            origin="bottom-left",
+        )
+        blck_bl_origin = ioclass_bl_origin.read_block()
+
+        self.assertAlmostEqual(
+            blck.segments[0].imagesequences[0][0][0, 0].magnitude,
+            blck_bl_origin.segments[0].imagesequences[0][0][49, 0].magnitude,  # since flipped over y, [0,0] == [49,0]
+            places=3,
+        )
+
         # end of directory
         shutil.rmtree(directory)
 
diff --git a/neo/test/rawiotest/common_rawio_test.py b/neo/test/rawiotest/common_rawio_test.py
@@ -34,12 +34,12 @@
     HAVE_DATALAD = True
 else:
     HAVE_DATALAD = False
-    # pytest skip doesn't explain why we are skipping. 
+    # pytest skip doesn't explain why we are skipping.
     # raise error if in CI to prevent tests from spuriously skipping and appearing
     # as passing.
-    if os.environ.get("GITHUB_ACTIONS") == 'true':
+    if os.environ.get("GITHUB_ACTIONS") == "true":
         raise RuntimeError("Datalad is required for running the CI.")
-    
+
 
 # url_for_tests = "https://portal.g-node.org/neo/" #This is the old place
 repo_for_test = default_testing_repo
diff --git a/neo/test/rawiotest/test_intanrawio.py b/neo/test/rawiotest/test_intanrawio.py
@@ -21,10 +21,9 @@ class TestIntanRawIO(
         "intan/intan_fpc_rhs_test_240329_091637/info.rhs",  # Format one-file-per-channel
         "intan/intan_fps_rhs_test_240329_091536/info.rhs",  # Format one-file-per-signal
         "intan/rhd_fpc_multistim_240514_082044/info.rhd",  # Multiple digital channels one-file-per-channel rhd
-        "intan/rhs_stim_data_single_file_format/intanTestFile.rhs", # header-attached rhs data with stimulus current
-        "intan/test_fcs_dc_250327_154333/info.rhs", # this is an example of only having dc amp rather than amp files
-        "intan/test_fpc_stim_250327_151617/info.rhs", # wrong files names Heberto will fix naimgin in the future
-
+        "intan/rhs_stim_data_single_file_format/intanTestFile.rhs",  # header-attached rhs data with stimulus current
+        "intan/test_fcs_dc_250327_154333/info.rhs",  # this is an example of only having dc amp rather than amp files
+        "intan/test_fpc_stim_250327_151617/info.rhs",  # wrong files names Heberto will fix naimgin in the future
     ]
 
     def test_annotations(self):
@@ -88,7 +87,9 @@ def test_correct_reading_one_file_per_channel_amplifiers(self):
         amplifier_stream_index = 0
         for channel_name, amplifier_file_path in zip(channel_names, amplifier_file_paths):
             data_raw = np.fromfile(amplifier_file_path, dtype=np.int16).squeeze()
-            data_from_neo = intan_reader.get_analogsignal_chunk(channel_ids=[channel_name], stream_index=amplifier_stream_index).squeeze()
+            data_from_neo = intan_reader.get_analogsignal_chunk(
+                channel_ids=[channel_name], stream_index=amplifier_stream_index
+            ).squeeze()
             np.testing.assert_allclose(data_raw, data_from_neo)
 
     def test_correct_reading_one_file_per_channel_rhs_stim(self):
@@ -101,42 +102,45 @@ def test_correct_reading_one_file_per_channel_rhs_stim(self):
         # This should be the folder where the files of all the channels are stored
         folder_path = file_path.parent
 
-        # The paths for the stim channels are stim-A-000.dat, stim-A-001.dat, stim-A-002.dat, 
+        # The paths for the stim channels are stim-A-000.dat, stim-A-001.dat, stim-A-002.dat,
         # Whereas the ids are A-001_STIM, A-002_STIM, A-003_STIM, etc
         stim_file_paths = [path for path in folder_path.iterdir() if "stim" in path.name]
         channel_ids = [f"{p.stem[5:]}_STIM" for p in stim_file_paths]
-        
-        stim_stream_index  = 2
+
+        stim_stream_index = 2
         for channel_id, amplifier_file_path in zip(channel_ids, stim_file_paths):
             data_raw = np.fromfile(amplifier_file_path, dtype=np.uint16)
             decoded_data = intan_reader._decode_current_from_stim_data(data_raw, 0, data_raw.shape[0])
-            data_from_neo = intan_reader.get_analogsignal_chunk(channel_ids=[channel_id], stream_index=stim_stream_index).squeeze()
+            data_from_neo = intan_reader.get_analogsignal_chunk(
+                channel_ids=[channel_id], stream_index=stim_stream_index
+            ).squeeze()
             np.testing.assert_allclose(decoded_data, data_from_neo)
 
-
     def test_correct_decoding_of_stimulus_current(self):
         # See https://github.com/NeuralEnsemble/python-neo/pull/1660 for discussion
-        # See https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/src/master/intan/README.md#rhs_stim_data_single_file_format 
-        # For a description of the data 
-        
+        # See https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/src/master/intan/README.md#rhs_stim_data_single_file_format
+        # For a description of the data
+
         file_path = Path(self.get_local_path("intan/rhs_stim_data_single_file_format/intanTestFile.rhs"))
         intan_reader = IntanRawIO(filename=file_path)
         intan_reader.parse_header()
-        
-        signal_streams = intan_reader.header['signal_streams']
-        stream_ids = signal_streams['id'].tolist()
-        stream_index = stream_ids.index('11')
+
+        signal_streams = intan_reader.header["signal_streams"]
+        stream_ids = signal_streams["id"].tolist()
+        stream_index = stream_ids.index("11")
         sampling_rate = intan_reader.get_signal_sampling_rate(stream_index=stream_index)
         sig_chunk = intan_reader.get_analogsignal_chunk(stream_index=stream_index, channel_ids=["D-016_STIM"])
-        final_stim = intan_reader.rescale_signal_raw_to_float(sig_chunk, stream_index=stream_index, channel_ids=["D-016_STIM"])
+        final_stim = intan_reader.rescale_signal_raw_to_float(
+            sig_chunk, stream_index=stream_index, channel_ids=["D-016_STIM"]
+        )
 
         # This contains only the first pulse and I got this by visual inspection
         data_to_test = final_stim[200:250]
-        
+
         positive_pulse_size = np.max(data_to_test).item()
         negative_pulse_size = np.min(data_to_test).item()
 
-        expected_value = 60 * 1e-6# 60 microamperes
+        expected_value = 60 * 1e-6  # 60 microamperes
 
         # Assert is close float
         assert np.isclose(positive_pulse_size, expected_value)
@@ -146,15 +150,15 @@ def test_correct_decoding_of_stimulus_current(self):
         argmin = np.argmin(data_to_test)
         argmax = np.argmax(data_to_test)
         assert argmin < argmax
-        
+
         # Check that the negative pulse is 200 us long
         negative_pulse_frames = np.where(data_to_test > 0)[0]
         number_of_negative_frames = negative_pulse_frames.size
         duration_of_negative_pulse = number_of_negative_frames / sampling_rate
 
-        expected_duration = 200 * 1e-6  # 400 microseconds / 2 
+        expected_duration = 200 * 1e-6  # 400 microseconds / 2
         assert np.isclose(duration_of_negative_pulse, expected_duration)
-        
+
         # Check that the positive pulse is 200 us long
         positive_pulse_frames = np.where(data_to_test > 0)[0]
         number_of_positive_frames = positive_pulse_frames.size
@@ -163,30 +167,31 @@ def test_correct_decoding_of_stimulus_current(self):
 
         assert np.isclose(duration_of_positive_pulse, expected_duration)
 
-
     def test_correct_decoding_of_stimulus_current(self):
         # See https://github.com/NeuralEnsemble/python-neo/pull/1660 for discussion
-        # See https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/src/master/intan/README.md#rhs_stim_data_single_file_format 
-        # For a description of the data 
-        
+        # See https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/src/master/intan/README.md#rhs_stim_data_single_file_format
+        # For a description of the data
+
         file_path = Path(self.get_local_path("intan/rhs_stim_data_single_file_format/intanTestFile.rhs"))
         intan_reader = IntanRawIO(filename=file_path)
         intan_reader.parse_header()
-        
-        signal_streams = intan_reader.header['signal_streams']
-        stream_ids = signal_streams['id'].tolist()
-        stream_index = stream_ids.index('11')
+
+        signal_streams = intan_reader.header["signal_streams"]
+        stream_ids = signal_streams["id"].tolist()
+        stream_index = stream_ids.index("11")
         sampling_rate = intan_reader.get_signal_sampling_rate(stream_index=stream_index)
         sig_chunk = intan_reader.get_analogsignal_chunk(stream_index=stream_index, channel_ids=["D-016_STIM"])
-        final_stim = intan_reader.rescale_signal_raw_to_float(sig_chunk, stream_index=stream_index, channel_ids=["D-016_STIM"])
+        final_stim = intan_reader.rescale_signal_raw_to_float(
+            sig_chunk, stream_index=stream_index, channel_ids=["D-016_STIM"]
+        )
 
         # This contains only the first pulse and I got this by visual inspection
         data_to_test = final_stim[200:250]
-        
+
         positive_pulse_size = np.max(data_to_test).item()
         negative_pulse_size = np.min(data_to_test).item()
 
-        expected_value = 60 * 1e-6# 60 microamperes
+        expected_value = 60 * 1e-6  # 60 microamperes
 
         # Assert is close float
         assert np.isclose(positive_pulse_size, expected_value)
@@ -196,15 +201,15 @@ def test_correct_decoding_of_stimulus_current(self):
         argmin = np.argmin(data_to_test)
         argmax = np.argmax(data_to_test)
         assert argmin < argmax
-        
+
         # Check that the negative pulse is 200 us long
         negative_pulse_frames = np.where(data_to_test > 0)[0]
         number_of_negative_frames = negative_pulse_frames.size
         duration_of_negative_pulse = number_of_negative_frames / sampling_rate
 
-        expected_duration = 200 * 1e-6  # 400 microseconds / 2 
+        expected_duration = 200 * 1e-6  # 400 microseconds / 2
         assert np.isclose(duration_of_negative_pulse, expected_duration)
-        
+
         # Check that the positive pulse is 200 us long
         positive_pulse_frames = np.where(data_to_test > 0)[0]
         number_of_positive_frames = positive_pulse_frames.size
diff --git a/neo/test/rawiotest/test_spikeglxrawio.py b/neo/test/rawiotest/test_spikeglxrawio.py
diff --git a/neo/test/rawiotest/tools.py b/neo/test/rawiotest/tools.py
