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Fix petab.visualize.data_overview.create_report #96

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merged 2 commits into from
Nov 30, 2021
Merged

Fix petab.visualize.data_overview.create_report #96

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92876b6
Fix petab.visualize.data_overview.create_report
dweindl Nov 30, 2021
16afc51
Merge branch 'develop' into fix_report
dweindl Nov 30, 2021
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14 changes: 7 additions & 7 deletions petab/visualize/data_overview.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,7 @@ def create_report(
template_file = "report.html"

data_per_observable = get_data_per_observable(problem.measurement_df)
num_conditions = (len(problem.condition_df.columns)
- 1 * (CONDITION_NAME in problem.condition_df.columns))
num_conditions = len(problem.condition_df.index)

# Setup template engine
import jinja2
Expand All @@ -55,17 +54,18 @@ def get_data_per_observable(measurement_df: pd.DataFrame) -> pd.DataFrame:
Arguments:
measurement_df: PEtab measurement data frame
Returns:
data_per_observable:
Pivot table with number of data points per observable and condition
Pivot table with number of data points per observable and condition
"""

my_measurements = measurement_df.copy()

my_measurements[PREEQUILIBRATION_CONDITION_ID].fillna('', inplace=True)
index = [SIMULATION_CONDITION_ID]
if PREEQUILIBRATION_CONDITION_ID in my_measurements:
my_measurements[PREEQUILIBRATION_CONDITION_ID].fillna('', inplace=True)
index.append(PREEQUILIBRATION_CONDITION_ID)

data_per_observable = pd.pivot_table(
my_measurements, values=MEASUREMENT, aggfunc='count',
index=[SIMULATION_CONDITION_ID, PREEQUILIBRATION_CONDITION_ID],
index=index,
columns=[OBSERVABLE_ID], fill_value=0)

# Add row and column sums
Expand Down