🎨 Replace print with logger.* or raise Exception

FCP-INDI · Feb 14, 2024 · 43f5f46 · 43f5f46
1 parent 8f368de
commit 43f5f46
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Showing 3 changed files with 147 additions and 24 deletions.
diff --git a/CPAC/utils/create_flame_model_files.py b/CPAC/utils/create_flame_model_files.py
@@ -1,3 +1,24 @@
+# Copyright (C) 2016-2024  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+from CPAC.utils.monitoring.custom_logging import getLogger
+
+logger = getLogger("nipype.workflow")
+
+
 def create_dummy_string(length):
     ppstring = ""
     for i in range(0, length):
@@ -126,6 +147,8 @@ def create_fts_file(ftest_list, con_names, model_name, current_output, out_dir):
 
     import numpy as np
 
+    logger.info("\nFound f-tests in your model, writing f-tests file (.fts)..\n")
+
     try:
         out_file = os.path.join(out_dir, model_name + ".fts")
 
@@ -202,7 +225,8 @@ def create_con_ftst_file(
     evs = evs.rstrip("\r\n").split(",")
 
     if evs[0].strip().lower() != "contrasts":
-        raise Exception
+        msg = "first cell in contrasts file should contain 'Contrasts'"
+        raise ValueError(msg)
 
     # remove "Contrasts" label and replace it with "Intercept"
     # evs[0] = "Intercept"
@@ -217,7 +241,8 @@ def create_con_ftst_file(
     try:
         contrasts_data = np.genfromtxt(con_file, names=True, delimiter=",", dtype=None)
     except:
-        raise Exception
+        msg = f"Could not successfully read in contrast file: {con_file}"
+        raise OSError(msg)
 
     lst = contrasts_data.tolist()
     # lst = list of rows of the contrast matrix (each row represents a
@@ -291,27 +316,31 @@ def create_con_ftst_file(
         fts_n = fts_columns.T
 
     if len(column_names) != (num_EVs_in_con_file):
-        "\n\n[!] CPAC says: The number of EVs in your model " "design matrix (found in the %s.mat file) does not " "match the number of EVs (columns) in your custom " "contrasts matrix CSV file.\n\nCustom contrasts matrix " "file: %s\n\nNumber of EVs in design matrix: %d\n" "Number of EVs in contrasts file: %d\n\nThe column " "labels in the design matrix should match those in " "your contrasts .CSV file.\nColumn labels in design " "matrix:\n%s" % (
+        logger.error(
+            "\n\n[!] CPAC says: The number of EVs in your model design matrix (found"
+            " in the %s.mat file) does not match the number of EVs (columns) in your"
+            " custom contrasts matrix CSV file.\n\nCustom contrasts matrix file:"
+            " %s\n\nNumber of EVs in design matrix: %d\nNumber of EVs in contrasts"
+            " file: %d\n\nThe column labels in the design matrix should match those in"
+            "your contrasts .CSV file.\nColumn labels in design matrix:\n%s",
             model_name,
             con_file,
             len(column_names),
             num_EVs_in_con_file,
             str(column_names),
         )
-
-        # raise Exception(err_string)
         return None, None
 
     for design_mat_col, con_csv_col in zip(column_names, evs[1:]):
         if con_csv_col not in design_mat_col:
-            errmsg = (
-                "\n\n[!] CPAC says: The names of the EVs in your "
-                "custom contrasts .csv file do not match the names or "
-                "order of the EVs in the design matrix. Please make "
-                "sure these are consistent.\nDesign matrix EV columns: "
-                "%s\nYour contrasts matrix columns: %s\n\n" % (column_names, evs[1:])
+            logger.error(
+                "\n\n[!] CPAC says: The names of the EVs in your custom contrasts .csv"
+                " file do not match the names or order of the EVs in the design"
+                " matrix. Please make sure these are consistent.\nDesign matrix EV"
+                " columns: %s\nYour contrasts matrix columns: %s\n\n",
+                column_names,
+                evs[1:],
             )
-
             return None, None
 
     out_file = os.path.join(output_dir, model_name + ".con")
@@ -344,6 +373,7 @@ def create_con_ftst_file(
 
     ftest_out_file = None
     if fTest:
+        logger.info("\nFound f-tests in your model, writing f-tests file (.fts)..\n")
         ftest_out_file = os.path.join(output_dir, model_name + ".fts")
 
         with open(ftest_out_file, "wt") as f:

diff --git a/CPAC/utils/create_fsl_flame_preset.py b/CPAC/utils/create_fsl_flame_preset.py
@@ -1,3 +1,23 @@
+# Copyright (C) 2018-2024  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+from CPAC.utils.monitoring.custom_logging import getLogger
+
+logger = getLogger("nipype.workflow")
+
 # TODO: create a function that can help easily map raw pheno files that do not
 # TODO: have the participant_session id that CPAC uses
 
@@ -56,7 +76,7 @@ def write_group_list_text_file(group_list, out_file=None):
             f.write(f"{part_id}\n")
 
     if os.path.exists(out_file):
-        pass
+        logger.info("Group-level analysis participant list written:\n%s\n", out_file)
 
     return out_file
 
@@ -83,7 +103,7 @@ def write_dataframe_to_csv(matrix_df, out_file=None):
     matrix_df.to_csv(out_file, index=False)
 
     if os.path.exists(out_file):
-        pass
+        logger.info("CSV file written:\n%s\n", out_file)
 
 
 def write_config_dct_to_yaml(config_dct, out_file=None):
@@ -170,7 +190,9 @@ def write_config_dct_to_yaml(config_dct, out_file=None):
                 )
 
     if os.path.exists(out_file):
-        pass
+        logger.info(
+            "Group-level analysis configuration YAML file written:\n%s\n", out_file
+        )
 
 
 def create_design_matrix_df(

diff --git a/CPAC/utils/create_fsl_model.py b/CPAC/utils/create_fsl_model.py
@@ -1,3 +1,24 @@
+# Copyright (C) 2012-2024  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+from CPAC.utils.monitoring.custom_logging import getLogger
+
+logger = getLogger("nipype.workflow")
+
+
 def load_pheno_file(pheno_file):
     import os
 
@@ -362,7 +383,13 @@ def model_group_var_separately(
     grouping_var, formula, pheno_data_dict, ev_selections, coding_scheme
 ):
     if grouping_var is None or grouping_var not in formula:
-        raise Exception
+        msg = (
+            "\n\n[!] CPAC says: Model group variances separately is enabled, but the"
+            " grouping variable set is either set to None, or was not included in the"
+            f" model as one of the EVs.\n\nDesign formula: {formula}\nGrouping"
+            f" variable: {grouping_var}\n\n"
+        )
+        raise ValueError(msg)
 
     # do this a little early for the grouping variable so that it doesn't
     # get in the way of doing this for the other EVs once they have the
@@ -471,18 +498,33 @@ def model_group_var_separately(
 def check_multicollinearity(matrix):
     import numpy as np
 
+    logger.info("\nChecking for multicollinearity in the model..")
+
     U, s, V = np.linalg.svd(matrix)
 
     max_singular = np.max(s)
     min_singular = np.min(s)
 
+    logger.info(
+        "Max singular: %s\nMin singular: %s\nRank: %s\n\n",
+        max_singular,
+        min_singular,
+        np.linalg.matrix_rank(matrix),
+    )
+
+    _warning = (
+        "[!] CPAC warns: Detected multicollinearity in the computed group-level"
+        " analysis model. Please double-check your model design.\n\n"
+    )
+
     if min_singular == 0:
-        pass
+        logger.warning(_warning)
 
     else:
         condition_number = float(max_singular) / float(min_singular)
+        logger.info("Condition number: %f\n\n", condition_number)
         if condition_number > 30:
-            pass
+            logger.warning(_warning)
 
 
 def write_mat_file(
@@ -805,8 +847,17 @@ def create_design_matrix(
     try:
         dmatrix = patsy.dmatrix(formula, pheno_data_dict, NA_action="raise")
 
-    except:
-        raise Exception
+    except Exception as e:
+        msg = (
+            "\n\n[!] CPAC says: Design matrix creation wasn't successful - do the"
+            " terms in your formula correctly correspond to the EVs listed in your"
+            " phenotype file?\nPhenotype file provided: %s\n\nPhenotypic data"
+            " columns (regressors): %s\nFormula: %s\n\n",
+            pheno_file,
+            list(pheno_data_dict.keys()),
+            formula,
+        )
+        raise RuntimeError(msg) from e
 
     # check the model for multicollinearity - Patsy takes care of this, but
     # just in case
@@ -976,6 +1027,8 @@ def create_dummy_string(length):
 def create_con_file(con_dict, col_names, file_name, current_output, out_dir):
     import os
 
+    logger.info("col names: %s", col_names)
+
     with open(os.path.join(out_dir, file_name) + ".con", "w+") as f:
         # write header
         num = 1
@@ -1012,6 +1065,7 @@ def create_fts_file(ftest_list, con_dict, model_name, current_output, out_dir):
     import numpy as np
 
     try:
+        logger.info("\nFound f-tests in your model, writing f-tests file (.fts)..\n")
         with open(os.path.join(out_dir, model_name + ".fts"), "w") as f:
             print("/NumWaves\t", len(con_dict), file=f)
             print("/NumContrasts\t", len(ftest_list), file=f)
@@ -1089,6 +1143,7 @@ def create_con_ftst_file(
     # evs[0] = "Intercept"
 
     fTest = False
+    logger.info("evs: %s", evs)
     for ev in evs:
         if "f_test" in ev:
             count_ftests += 1
@@ -1099,8 +1154,9 @@ def create_con_ftst_file(
     try:
         data = np.genfromtxt(con_file, names=True, delimiter=",", dtype=None)
 
-    except:
-        raise Exception
+    except Exception as e:
+        msg = f"Error: Could not successfully read in contrast file: {con_file}"
+        raise OSError(msg) from e
 
     lst = data.tolist()
 
@@ -1218,6 +1274,7 @@ def create_con_ftst_file(
         np.savetxt(f, contrasts, fmt="%1.5e", delimiter="\t")
 
     if fTest:
+        logger.info("\nFound f-tests in your model, writing f-tests file (.fts)..\n")
         ftest_out_dir = os.path.join(output_dir, model_name + ".fts")
 
         with open(ftest_out_dir, "wt") as f:
@@ -1361,8 +1418,13 @@ def run(
     try:
         if not os.path.exists(output_dir):
             os.makedirs(output_dir)
-    except:
-        raise Exception
+    except Exception as e:
+        msg = (
+            "\n\n[!] CPAC says: Could not successfully create the group analysis"
+            f" output directory:\n{output_dir}\n\nMake sure you have write access"
+            " in this file structure.\n\n\n"
+        )
+        raise OSError(msg) from e
 
     measure_dict = {}
 
@@ -1551,6 +1613,10 @@ def run(
         or (custom_contrasts == "")
         or ("None" in custom_contrasts)
     ):
+        logger.info(
+            "Writing contrasts file (.con) based on contrasts provided using the group"
+            " analysis model builder's contrasts editor.."
+        )
         create_con_file(
             contrasts_dict, regressor_names, model_name, current_output, model_out_dir
         )
@@ -1561,6 +1627,11 @@ def run(
             )
 
     else:
+        logger.info(
+            "\nWriting contrasts file (.con) based on contrasts provided with a custom"
+            " contrasts matrix CSV file..\n"
+        )
+
         create_con_ftst_file(
             custom_contrasts,
             model_name,