Merge branch 'main' into js_fix_passed_wells

Author: joeyshuttleworth

pcpostprocess/detect_ramp_bounds.py

@@ -1,23 +1,23 @@
 import numpy as np
 
 
-def detect_ramp_bounds(times, voltage_sections, ramp_no=0):
+def detect_ramp_bounds(times, voltage_sections, ramp_index=0):
     """
-    Extract the the times at the start and end of the nth ramp in the protocol.
+    Extract the timepoint indices at the start and end of the nth ramp in the protocol.
 
     @param times: np.array containing the time at which each sample was taken
     @param voltage_sections 2d np.array where each row describes a segment of the protocol: (tstart, tend, vstart, end)
-    @param ramp_no: the index of the ramp to select. Defaults to 0 - the first ramp
+    @param ramp_index: the index of the ramp to select. Defaults to 0 - the first ramp
 
-    @returns tstart, tend: the start and end times for the ramp_no+1^nth ramp
+    @returns istart, iend: the start and end timepoint indices for the specified ramp
     """
 
     ramps = [(tstart, tend, vstart, vend) for tstart, tend, vstart, vend
              in voltage_sections if vstart != vend]
     try:
-        ramp = ramps[ramp_no]
+        ramp = ramps[ramp_index]
     except IndexError:
-        print(f"Requested {ramp_no+1}th ramp (ramp_no={ramp_no}),"
+        print(f"Requested {ramp_index+1}th ramp (ramp_index={ramp_index}),"
               " but there are only {len(ramps)} ramps")
 
     tstart, tend = ramp[:2]

pcpostprocess/directory_builder.py

@@ -0,0 +1,63 @@
+import datetime
+import os
+import sys
+
+from ._version import __commit_id__, __version__
+
+
+def get_git_revision_hash():
+    """
+    Get the hash for the git commit currently being used.
+
+    @return The most recent commit hash or a suitable message
+
+    """
+
+    return __commit_id__
+
+
+def get_build_type():
+    if "dev" in __version__:
+        return "Develop"
+    else:
+        return "Release"
+
+
+def setup_output_directory(dirname: str = None, subdir_name: str = None):
+    """
+    Create an output directory if one doesn't already exist. Place an info
+    file in this directory which lists the date/time created, the version of
+    pcpostprocess, the command-line arguments provided, and the most recent git
+    commit. The two parameters allow for a user specified top-level directory and
+    a script-defined name for a subdirectory.
+
+    @param Optional directory name
+    @param Optional subdirectory name
+
+    @return The path to the created file directory (String)
+    """
+
+    if dirname is None:
+        if subdir_name:
+            dirname = os.path.join("output", f"{subdir_name}")
+        else:
+            dirname = os.path.join("output", "output")
+
+    if subdir_name is not None:
+        dirname = os.path.join(dirname, subdir_name)
+    if not os.path.exists(dirname):
+        os.makedirs(dirname)
+
+    with open(os.path.join(dirname, "pcpostprocess_info.txt"), "w") as description_fout:
+        git_hash = get_git_revision_hash()
+        datetimestr = str(datetime.datetime.now())
+        description_fout.write("pcpostprocess output "
+                               "https://github.com/CardiacModelling/pcpostprocess\n")
+        description_fout.write(f"Date: {datetimestr}\n")
+        description_fout.write(f"Version: {__version__}\n")
+        description_fout.write(f"Build type: {get_build_type()}\n")
+        description_fout.write(f"Commit: {git_hash}\n")
+        command = " ".join(sys.argv)
+        description_fout.write(f"Command: {command}\n")
+    return dirname
+

pcpostprocess/infer_reversal.py

@@ -33,10 +33,7 @@ def infer_reversal_potential(current, times, voltage_segments, voltages,
     """
 
     # Get ramp bounds, assuming final ramp is the reversal ramp
-    tstart, tend = detect_ramp_bounds(times, voltage_segments, -1)
-
-    istart = np.argmax(times > tstart)
-    iend = np.argmax(times > tend)
+    istart, iend = detect_ramp_bounds(times, voltage_segments, -1)
 
     current = current[istart:iend]
     voltages = voltages[istart:iend]

pcpostprocess/leak_correct.py

@@ -149,7 +149,7 @@ def fit_linear_leak(current, voltage, times, ramp_start_index, ramp_end_index,
         ax4.plot(times, I_obs, label=r'$I_\mathrm{obs}$')
         ax4.plot(times, I_leak, linestyle='--', label=r'$I_\mathrm{L}$')
         ax4.plot(times, I_obs - I_leak,
-                 linestyle='--', alpha=0.5, label=r'$I_\mathrm{obs} - I_\mathrm{L}$')
+                 alpha=0.5, label=r'$I_\mathrm{obs} - I_\mathrm{L}$')
         ax4.legend(frameon=False)
 
         if not os.path.exists(output_dir):