Skip to content

"Fix" summarise-herg-qc #119

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
MichaelClerx wants to merge 2 commits into from
+21 −20
Closed

"Fix" summarise-herg-qc #119

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
96ab58f
Removed failing bits in summarise-herg-qc
MichaelClerx Nov 12, 2025
9cd93ed
Style fixes
MichaelClerx Nov 12, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
41 changes: 21 additions & 20 deletions pcpostprocess/scripts/summarise_herg_export.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ def main():
parser.add_argument('--protocols', type=str, default=[], nargs='+')
parser.add_argument('-r', '--reversal', type=float, default=np.nan)
# parser.add_argument('--selection_file', default=None, type=str)
parser.add_argument('--experiment_name', default='newtonrun4')
parser.add_argument('--experiment_name', default='13112023_MW2')
parser.add_argument('--figsize', type=int, nargs=2, default=[5, 3])
parser.add_argument('--output_all', action='store_true')
parser.add_argument('--log_level', default='INFO')
Expand Down Expand Up @@ -88,8 +88,8 @@ def main():
qc_styled_df.to_excel(os.path.join(output_dir, 'qc_table.xlsx'))
qc_styled_df.to_latex(os.path.join(output_dir, 'qc_table.tex'))

qc_estimates_file = os.path.join(args.save_dir, f"{args.experiment_name}_subtraction_qc.csv")
qc_vals_df = pd.read_csv(os.path.join(qc_estimates_file))
# qc_estimates_file = os.path.join(args.save_dir, f"{args.experiment_name}_subtraction_qc.csv")
# qc_vals_df = pd.read_csv(os.path.join(qc_estimates_file))

qc_df.protocol = ['staircaseramp1' if protocol == 'staircaseramp' else protocol
for protocol in qc_df.protocol]
Expand Down Expand Up @@ -131,9 +131,8 @@ def main():
categories=protocol_order,
ordered=True)

qc_vals_df['protocol'] = pd.Categorical(qc_vals_df['protocol'],
categories=protocol_order,
ordered=True)
# qc_vals_df['protocol'] = pd.Categorical(
# qc_vals_df['protocol'], categories=protocol_order, ordered=True)

leak_parameters_df.sort_values(['protocol', 'sweep'], inplace=True)
except FileNotFoundError as exc:
Expand Down Expand Up @@ -161,10 +160,10 @@ def main():
plot_spatial_Erev(leak_parameters_df)

leak_parameters_df['passed QC'] = [well in passed_wells for well in leak_parameters_df.well]
qc_vals_df['passed QC'] = [well in passed_wells for well in qc_vals_df.well]
# qc_vals_df['passed QC'] = [well in passed_wells for well in qc_vals_df.well]

# do_scatter_matrices(leak_parameters_df, qc_vals_df)
plot_histograms(leak_parameters_df, qc_vals_df)
plot_histograms(leak_parameters_df)

# Very resource intensive
# overlay_reversal_plots(leak_parameters_df)
Expand Down Expand Up @@ -701,7 +700,7 @@ def plot_spatial_passed(df):
plt.close(fig)


def plot_histograms(df, qc_df):
def plot_histograms(df):
fig = plt.figure(figsize=args.figsize, constrained_layout=True)
ax = fig.subplots()

Expand Down Expand Up @@ -896,20 +895,22 @@ def create_attrition_table(qc_df, subtraction_df):
'qc6.subtracted', 'qc6.1.subtracted',
'qc6.2.subtracted']

subtraction_df_sc = subtraction_df[subtraction_df.protocol.isin(['staircaseramp1',
'staircaseramp1_2'])]
R_leftover_qc = subtraction_df_sc.groupby('well')['R_leftover'].max() < 0.4
# subtraction_df_sc = subtraction_df[
# subtraction_df.protocol.isin(['staircaseramp1', 'staircaseramp1_2'])]

qc_df['QC.R_leftover'] = [R_leftover_qc.loc[well] for well in subtraction_df.well.unique()]
# R_leftover_qc = subtraction_df_sc.groupby('well')['R_leftover'].max() < 0.4

# This line doesn't work: "Length of values does not match length of index"
# qc_df['QC.R_leftover'] = [R_leftover_qc.loc[well] for well in subtraction_df.well.unique()]

stage_3_criteria = original_qc_criteria + ['QC1.all_protocols', 'QC4.all_protocols',
'QC6.all_protocols']
stage_4_criteria = stage_3_criteria + ['qc3.bookend']
stage_5_criteria = stage_4_criteria + ['QC.Erev.all_protocols', 'QC.Erev.spread']

stage_6_criteria = stage_5_criteria + ['QC.R_leftover']
# stage_6_criteria = stage_5_criteria + ['QC.R_leftover']

agg_dict = {crit: 'min' for crit in stage_6_criteria}
agg_dict = {crit: 'min' for crit in stage_5_criteria}

qc_df_sc1 = qc_df[qc_df.protocol == 'staircaseramp1']
print(qc_df_sc1.values.shape)
Expand All @@ -935,11 +936,11 @@ def create_attrition_table(qc_df, subtraction_df):
.agg(agg_dict)[stage_5_criteria].values,
axis=1))

n_stage_6_wells = np.sum(np.all(qc_df.groupby('well')
.agg(agg_dict)[stage_6_criteria].values,
axis=1))
# n_stage_6_wells = np.sum(np.all(qc_df.groupby('well')
# .agg(agg_dict)[stage_6_criteria].values,
# axis=1))

passed_qc_df = qc_df.groupby('well').agg(agg_dict)[stage_6_criteria]
passed_qc_df = qc_df.groupby('well').agg(agg_dict)[stage_5_criteria]
print(passed_qc_df)
passed_wells = [well for well, row in passed_qc_df.iterrows() if np.all(row.values)]

Expand All @@ -951,7 +952,7 @@ def create_attrition_table(qc_df, subtraction_df):
'stage3': [n_stage_3_wells],
'stage4': [n_stage_4_wells],
'stage5': [n_stage_5_wells],
'stage6': [n_stage_6_wells],
# 'stage6': [n_stage_6_wells],
}

res_df = pd.DataFrame.from_records(res_dict)
Expand Down