Minor refactor in engine functions

README.md

@@ -22,7 +22,7 @@ To work with probtest, a configuration file is needed. This file contains all th
 
 ### perturb
 
-Perturbs netcdf files that can be used as input by the model.
+Creates an ensemble of netcdf files that can be used as input by the model.
 
 ### run-ensemble
 

engine/cdo_table.py

@@ -19,6 +19,7 @@
 from util.dataframe_ops import df_from_file_ids
 from util.file_system import file_names_from_pattern
 from util.log_handler import logger
+from util.utils import prepend_type_to_member_id
 
 
 def compute_rel_diff(var1, var2):
@@ -126,11 +127,7 @@ def cdo_table(
     cdo_table_file,
     file_specification,
 ):  # pylint: disable=too-many-positional-arguments
-
-    if member_type:
-        member_id_str = member_type + "_" + str(member_id)
-    else:
-        member_id_str = str(member_id)
+
 
     file_specification = file_specification[0]  # can't store dicts as defaults in click
     assert isinstance(file_specification, dict), "must be dict"
@@ -142,6 +139,7 @@ def cdo_table(
 
     # step 1: compute rel-diff netcdf files
     with tempfile.TemporaryDirectory() as tmpdir:
+        complete_member_id = prepend_type_to_member_id(member_type, member_id)
         for _, file_pattern in file_id:
             ref_files, err = file_names_from_pattern(model_output_dir, file_pattern)
             if err > 0:
@@ -151,7 +149,7 @@ def cdo_table(
                 continue
             ref_files.sort()
             perturb_files, err = file_names_from_pattern(
-                perturbed_model_output_dir.format(member_id=member_id_str), file_pattern
+                perturbed_model_output_dir.format(member_id=complete_member_id), file_pattern
             )
             if err > 0:
                 logger.info(
@@ -165,7 +163,7 @@ def cdo_table(
                     continue
                 ref_data = xr.open_dataset(f"{model_output_dir}/{rf}")
                 perturb_data = xr.open_dataset(
-                    f"{perturbed_model_output_dir.format(member_id=member_id_str)}/{pf}"
+                    f"{perturbed_model_output_dir.format(member_id=complete_member_id)}/{pf}"
                 )
                 diff_data = ref_data.copy()
                 varnames = [

engine/check.py

@@ -12,7 +12,7 @@
 import click
 
 from util.click_util import cli_help
-from util.dataframe_ops import check_stats_file_with_tolerances, compute_div_dataframe
+from util.dataframe_ops import check_stats_file_with_tolerances, compute_division_df
 from util.log_handler import logger
 
 
@@ -40,8 +40,6 @@ def check(input_file_ref, input_file_cur, tolerance_file_name, factor):
         tolerance_file_name, input_file_ref, input_file_cur, factor
     )
 
-    div = compute_div_dataframe(err, tol)
-
     if out:
         logger.info("RESULT: check PASSED!")
     else:
@@ -51,6 +49,8 @@ def check(input_file_ref, input_file_cur, tolerance_file_name, factor):
         logger.info("\nTolerance")
         logger.info(tol)
         logger.info("\nError relative to tolerance")
-        logger.info(div)
+        logger.info(
+            compute_division_df(err, tol)
+        )
 
     sys.exit(0 if out else 1)

engine/perturb.py

@@ -5,7 +5,7 @@
 - Creating copies of specified model files and optionally copying all files from
   a source directory to a destination directory.
 - Applying perturbations to arrays in NetCDF files based on a specified
-  amplitude and random seed.
+  perturbation amplitude and random seed.
 """
 
 import os
@@ -17,35 +17,15 @@
 from util.click_util import CommaSeperatedInts, CommaSeperatedStrings, cli_help
 from util.log_handler import logger
 from util.netcdf_io import nc4_get_copy
-from util.utils import get_seed_from_member_id
+from util.utils import get_seed_from_member_id, prepend_type_to_member_id
 
 
-def create_perturb_files(in_path, in_files, out_path, copy_all_files=False):
-    path = os.path.abspath(in_path)
-    if not os.path.exists(out_path):
-        logger.info("creating new directory: %s", out_path)
-        os.makedirs(out_path)
-    data = [nc4_get_copy(f"{path}/{f}", f"{out_path}/{f}") for f in in_files]
-
-    if copy_all_files:
-        all_files = os.listdir(path)
-        # disregard the input files which are copied above
-        other_files = [f for f in all_files if f not in in_files]
-        # copy all other files
-        for f in other_files:
-            shutil.copy(f"{in_path}/{f}", out_path)
-
-    return data
-
-
-def perturb_array(array, s, a):
-    shape = array.shape
-    np.random.seed(s)
-    p = (
-        np.random.rand(*shape) * 2 - 1
-    ) * a + 1  # *2-1: map to [-1,1), *a: rescale to amplitude, +1 perturb around 1
-    parray = np.copy(array * p)
-    return parray
+def perturb_array(array, seed, perturb_amplitude):
+    np.random.seed(seed)
+    perturbation = (
+        np.random.rand(*array.shape) * 2 - 1
+    ) * perturb_amplitude + 1  # *2-1: map to [-1,1), *perturb_amplitude: rescale to perturbation amplitude, +1 perturb around 1
+    return np.copy(array * perturbation)
 
 
 @click.command()
@@ -102,29 +82,37 @@ def perturb(
     copy_all_files,
 ):  # pylint: disable=unused-argument, too-many-positional-arguments
 
-    for m_id in member_ids:
+    for member_id in member_ids:
 
-        if member_type:
-            m_id_str = member_type + "_" + str(m_id)
-        else:
-            m_id_str = str(m_id)
-
-        perturbed_model_input_dir_member_id = perturbed_model_input_dir.format(
-            member_id=m_id_str
-        )
-
-        data = create_perturb_files(
-            model_input_dir,
-            files,
-            perturbed_model_input_dir_member_id,
-            copy_all_files,
+        perturbed_dir = perturbed_model_input_dir.format(
+            member_id=prepend_type_to_member_id(member_type, member_id)
         )
+
+        model_input_dir_abspath = os.path.abspath(model_input_dir)
+
+        # Create directory for perturbed ensemble member 
+        if not os.path.exists(perturbed_dir):
+            logger.info("creating new directory: %s", perturbed_dir)
+            os.makedirs(perturbed_dir)
+
+        # Add perturbed files to member directory
+        data = [
+            nc4_get_copy(
+                f"{model_input_dir_abspath}/{f}", f"{perturbed_dir}/{f}"
+            ) for f in files
+        ]
 
         for d in data:
             for vn in variable_names:
                 d.variables[vn][:] = perturb_array(
-                    d.variables[vn][:],
-                    get_seed_from_member_id(m_id),
-                    perturb_amplitude,
+                    array=d.variables[vn][:],
+                    seed=get_seed_from_member_id(member_id),
+                    perturb_amplitude=perturb_amplitude,
                 )
             d.close()
+
+        # Copy rest of the files in `model_input_dir` to the perturbed ensemble member dir (`perturbed_dir`)
+        if copy_all_files:
+            for f in os.listdir(model_input_dir_abspath):
+                if f not in files: # files added manually via `files` flag already copied above
+                    shutil.copy(os.path.join(model_input_dir, f), perturbed_dir)

engine/run_ensemble.py

@@ -17,15 +17,7 @@
 
 from util.click_util import CommaSeperatedInts, CommaSeperatedStrings, cli_help
 from util.log_handler import logger
-from util.utils import get_seed_from_member_id
-
-
-def is_float(string):
-    try:
-        float(string)
-        return True
-    except ValueError:
-        return False
+from util.utils import get_seed_from_member_id, prepend_type_to_member_id
 
 
 # replace an assignment statement (left=*right* to left=new)
@@ -234,33 +226,30 @@ def run_ensemble(
         append_job(job, job_list, parallel)
 
     # run the ensemble
-    for m_id in member_ids:
+    for member_id in member_ids:
 
-        Path(perturbed_run_dir.format(member_id=str(m_id))).mkdir(
+        Path(perturbed_run_dir.format(member_id=str(member_id))).mkdir(
             exist_ok=True, parents=True
         )
-        os.chdir(perturbed_run_dir.format(member_id=str(m_id)))
-
-        if member_type:
-            m_id_str = member_type + "_" + str(m_id)
-        else:
-            m_id_str = str(m_id)
+        os.chdir(perturbed_run_dir.format(member_id=str(member_id)))
 
         runscript = f"{run_dir}/{run_script_name}"
+
+        complete_member_id = prepend_type_to_member_id(member_type, member_id)
 
-        perturbed_run_dir_path = perturbed_run_dir.format(member_id=m_id_str)
-        perturbed_run_script_path = perturbed_run_script_name.format(member_id=m_id_str)
+        perturbed_run_dir_path = perturbed_run_dir.format(member_id=complete_member_id)
+        perturbed_run_script_path = perturbed_run_script_name.format(member_id=complete_member_id)
         perturbed_runscript = f"{perturbed_run_dir_path}/{perturbed_run_script_path}"
 
         prepare_perturbed_run_script(
             runscript,
             perturbed_runscript,
             experiment_name,
-            perturbed_experiment_name.format(member_id=m_id_str),
+            perturbed_experiment_name.format(member_id=complete_member_id),
             lhs,
             rhs_new,
             rhs_old,
-            get_seed_from_member_id(m_id),
+            get_seed_from_member_id(member_id),
         )
 
         if not dry:

engine/stats.py

@@ -3,7 +3,6 @@
 
 This command line tool provides functionality for:
 - Creating and saving statistics dataframes from specified model output files.
-- Verifying that lists of values are monotonically increasing.
 - Generating statistics for both ensemble and reference model runs.
 """
 
@@ -16,10 +15,7 @@
 from util.click_util import CommaSeperatedInts, cli_help
 from util.dataframe_ops import df_from_file_ids
 from util.log_handler import logger
-
-
-def monotonically_increasing(li):
-    return all(x <= y for x, y in zip(li[:-1], li[1:]))
+from util.utils import prepend_type_to_member_id
 
 
 def create_stats_dataframe(input_dir, file_id, stats_file_name, file_specification):
@@ -33,31 +29,6 @@ def create_stats_dataframe(input_dir, file_id, stats_file_name, file_specificati
     return df
 
 
-def process_member(
-    member_id,
-    member_type,
-    model_output_dir,
-    perturbed_model_output_dir,
-    file_id,
-    stats_file_name,
-    file_specification,
-):  # pylint: disable=too-many-positional-arguments
-    if member_id == 0:
-        input_dir = model_output_dir
-        m_id_str = "ref"
-    else:
-        m_id_str = str(member_id)
-        if member_type:
-            m_id_str = member_type + "_" + m_id_str
-        input_dir = perturbed_model_output_dir.format(member_id=m_id_str)
-    create_stats_dataframe(
-        input_dir,
-        file_id,
-        stats_file_name.format(member_id=m_id_str),
-        file_specification,
-    )
-
-
 @click.command()
 @click.option(
     "--ensemble/--no-ensemble",
@@ -116,21 +87,29 @@ def stats(
 
     # compute stats for the ensemble and the reference run
     if ensemble:
+        df_args = []
+
         member_ids.append(0)
-        with Pool() as p:
-            args = [
+        for member_id in member_ids:
+            if member_id == 0:
+                complete_member_id = "ref"
+                output_dir = model_output_dir
+            else:
+                complete_member_id = prepend_type_to_member_id(member_type, member_id)
+                output_dir = perturbed_model_output_dir.format(member_id=complete_member_id)
+
+            df_args.append(
                 (
-                    m_id,
-                    member_type,
-                    model_output_dir,
-                    perturbed_model_output_dir,
+                    output_dir,
                     file_id,
-                    stats_file_name,
-                    file_specification,
+                    stats_file_name.format(member_id=complete_member_id),
+                    file_specification
                 )
-                for m_id in member_ids
-            ]
-            p.starmap(process_member, args)
+            )
+
+        with Pool() as p:
+            p.starmap(create_stats_dataframe, df_args)
+
     else:
         create_stats_dataframe(
             model_output_dir,

tests/util/test_utils.py

@@ -4,7 +4,7 @@
 
 import pytest
 
-from util.utils import get_seed_from_member_id
+from util.utils import get_seed_from_member_id, prepend_type_to_member_id
 
 
 def test_get_seed_from_member_id_invalid():
@@ -36,3 +36,6 @@ def test_get_seed_from_member_id_unique_seeds():
     """
     seeds = [get_seed_from_member_id(i) for i in range(1, 121)]
     assert len(seeds) == len(set(seeds)), "Seeds are not unique!"
+
+def test_prepend_type_to_member_id():
+    assert prepend_type_to_member_id("double", 3) == "double_3"

util/dataframe_ops.py

@@ -38,7 +38,7 @@ def compute_rel_diff_dataframe(df1, df2):
     return out
 
 
-def compute_div_dataframe(df1, df2):
+def compute_division_df(df1, df2):
     # avoid division by 0 and put nan instead
     out = df1 / df2.replace({0: np.nan})
     # put 0 if numerator is 0 as well

util/utils.py

@@ -13,6 +13,9 @@ def unique_elements(inlist):
             unique.append(element)
     return unique
 
+def prepend_type_to_member_id(member_type, member_id):
+    return (member_type + "_" + str(member_id)) if member_type else str(member_id)
+
 
 def first_idx_of(li, el):
     return li.index(el)