Merge branch 'master' into drop-old-numpy

Author: zm711

neo/io/tiffio.py

@@ -90,7 +90,7 @@ def __init__(
         units=None,
         sampling_rate=None,
         spatial_scale=None,
-        origin='top-left',
+        origin="top-left",
         **kwargs,
     ):
         # this block is because people might be confused about the PIL -> pillow change
@@ -99,8 +99,8 @@ def __init__(
             import PIL
         except ImportError:
             raise ImportError("To use TiffIO you must first `pip install pillow`")
-        
-        if origin != 'top-left' and origin != 'bottom-left':
+
+        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)

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"]

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
     ]
 
 

neo/test/iotest/test_tiffio.py

@@ -41,14 +41,14 @@ def test_read_group_of_tiff_grayscale(self):
             units="V",
             sampling_rate=1.0 * pq.Hz,
             spatial_scale=1.0 * pq.micrometer,
-            origin='bottom-left',
+            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, 
+            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

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

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

neo/test/rawiotest/test_spikeglxrawio.py

@@ -45,16 +45,21 @@ class TestSpikeGLXRawIO(BaseTestRawIO, unittest.TestCase):
 
     def test_loading_only_one_probe_in_multi_probe_scenario(self):
         from pathlib import Path
-        local_path_multi_probe_path = Path(self.get_local_path("spikeglx/multi_trigger_multi_gate/SpikeGLX/5-19-2022-CI0"))
+
+        local_path_multi_probe_path = Path(
+            self.get_local_path("spikeglx/multi_trigger_multi_gate/SpikeGLX/5-19-2022-CI0")
+        )
         gate_folder_path = local_path_multi_probe_path / "5-19-2022-CI0_g0"
         probe_folder_path = gate_folder_path / "5-19-2022-CI0_g0_imec1"
-        
+
         rawio = SpikeGLXRawIO(probe_folder_path)
         rawio.parse_header()
-        
+
         expected_stream_names = ["imec1.ap", "imec1.lf"]
         actual_stream_names = rawio.header["signal_streams"]["name"].tolist()
-        assert actual_stream_names == expected_stream_names, f"Expected {expected_stream_names}, but got {actual_stream_names}" 
+        assert (
+            actual_stream_names == expected_stream_names
+        ), f"Expected {expected_stream_names}, but got {actual_stream_names}"
 
     def test_with_location(self):
         rawio = SpikeGLXRawIO(self.get_local_path("spikeglx/Noise4Sam_g0"), load_channel_location=True)

neo/test/rawiotest/tools.py

@@ -18,7 +18,7 @@ def can_use_network():
     # env variable for local dev
     if os.environ.get("NEO_TESTS_NO_NETWORK", False):
         return False
-    
+
     # check for datalad presence
     datalad_spec = importlib.util.find_spec("datalad")
     if datalad_spec is not None:
@@ -28,5 +28,5 @@ def can_use_network():
 
     if not HAVE_DATALAD:
         return False
-    
+
     return True