lint

.gitignore

@@ -146,4 +146,5 @@ dmypy.json
 **/*original_timestamps.npy
 **/*qc.pdf
 **/*temporal_alignment.png
+**/*harp_line_search.png
 **/*ephys-rig-QC_output.txt

src/aind_ephys_rig_qc/generate_report.py

@@ -33,7 +33,7 @@ def generate_qc_report(
     timestamp_alignment_method="local",
     original_timestamp_filename="original_timestamps.npy",
     num_chunks=3,
-    plot_drift_map=True
+    plot_drift_map=True,
 ):
     """
     Generates a PDF report from an Open Ephys data directory
@@ -138,7 +138,9 @@ def generate_qc_report(
             else:
                 print("Local timestamps was not overwritten.")
 
-    create_qc_plots(pdf, directory, num_chunks=num_chunks, plot_drift_map=plot_drift_map)
+    create_qc_plots(
+        pdf, directory, num_chunks=num_chunks, plot_drift_map=plot_drift_map
+    )
 
     pdf.output(os.path.join(directory, report_name))
 
@@ -249,8 +251,12 @@ def get_event_info(events, stream_name):
 
 
 def create_qc_plots(
-    pdf, directory, num_chunks=3, raw_chunk_size=1000, psd_chunk_size=10000,
-    plot_drift_map=True
+    pdf,
+    directory,
+    num_chunks=3,
+    raw_chunk_size=1000,
+    psd_chunk_size=10000,
+    plot_drift_map=True,
 ):
     """
     Create QC plots for an Open Ephys data directory

src/aind_ephys_rig_qc/pdf_utils.py

@@ -56,7 +56,7 @@ def set_matplotlib_defaults(self):
         if platform.system() == "Linux":
             plt.rcParams["font.sans-serif"] = ["Nimbus Sans"]
         else:
-            plt.rcParams["font.sans-serif"] = ["Arial"] # pragma: no cover
+            plt.rcParams["font.sans-serif"] = ["Arial"]  # pragma: no cover
 
     def embed_figure(self, fig, width=190):
         """

src/aind_ephys_rig_qc/temporal_alignment.py

@@ -205,9 +205,7 @@ def search_harp_line(recording, directory, pdf=None):
                 + f"short interval perc {p_short[line_ind]:.2f}"
             )
         else:
-            ax2.set_title(
-                f"{p_value[line_ind]:.2f}, {p_short[line_ind]:.2f}"
-            )
+            ax2.set_title(f"{p_value[line_ind]:.2f}, {p_short[line_ind]:.2f}")
 
     # pick the line with even distribution overtime
     # and has short inter-event interval

tests/test_generate_report.py

@@ -37,15 +37,25 @@ def test_generate_report_harp(self, mock_input):
         """Check if output is pdf."""
         directory = str(test_folder / test_dataset)
         report_name = "qc.pdf"
-        generate_qc_report(directory, report_name, timestamp_alignment_method="harp", plot_drift_map=False)
+        generate_qc_report(
+            directory,
+            report_name,
+            timestamp_alignment_method="harp",
+            plot_drift_map=False,
+        )
         self.assertTrue(os.path.exists(os.path.join(directory, report_name)))
 
     @patch("builtins.input", return_value="n")
     def test_generate_report_harp_not_overwriting(self, mock_input):
         """Check if output is pdf."""
         directory = str(test_folder / test_dataset)
         report_name = "qc.pdf"
-        generate_qc_report(directory, report_name, timestamp_alignment_method="harp", plot_drift_map=False)
+        generate_qc_report(
+            directory,
+            report_name,
+            timestamp_alignment_method="harp",
+            plot_drift_map=False,
+        )
         self.assertTrue(os.path.exists(os.path.join(directory, report_name)))
 
     @patch("builtins.input", return_value="n")