From b48e9acb50b856b148c720e6d235e479eac4ab33 Mon Sep 17 00:00:00 2001
From: Mats <mats.vanes@psych.ox.ac.uk>
Date: Tue, 7 Jan 2025 14:49:24 +0000
Subject: [PATCH 01/10] add glm wrappers to preproc module

---
 osl_ephys/preprocessing/batch.py        |  28 +++-
 osl_ephys/preprocessing/osl_wrappers.py | 208 +++++++++++++++++++++++-
 2 files changed, 234 insertions(+), 2 deletions(-)

diff --git a/osl_ephys/preprocessing/batch.py b/osl_ephys/preprocessing/batch.py
index ee41e82..61ab5f9 100644
--- a/osl_ephys/preprocessing/batch.py
+++ b/osl_ephys/preprocessing/batch.py
@@ -459,7 +459,7 @@ def write_dataset(dataset, outbase, run_id, ftype='preproc-raw', overwrite=False
         outnames = {"raw": outbase.format(run_id=run_id, ftype=ftype, fext="fif")}
         if Path(outnames["raw"]).exists() and not overwrite:
             raise ValueError(
-                "{} already exists. Please delete or do use overwrite=True.".format(fif_outname)
+                "{} already exists. Please delete or do use overwrite=True.".format(outnames['raw'])
             )
         logger.info(f"Saving dataset['raw'] as {outnames['raw']}")
         dataset["raw"].save(outnames['raw'], overwrite=overwrite)   
@@ -494,6 +494,14 @@ def write_dataset(dataset, outbase, run_id, ftype='preproc-raw', overwrite=False
         logger.info(f"Saving dataset['glm'] as {outnames['glm']}")
         dataset["glm"].save_pkl(outnames['glm'], overwrite=overwrite)
     
+    if "fig" in dataset and "fig" not in skip and dataset['fig'] is not None:
+        keys = dataset["fig"].keys()
+        outnames['fig'] = {}
+        for key in keys:
+            outnames['fig'][key] = outbase.format(run_id=run_id, ftype=key, fext="png")
+            logger.info(f"Saving dataset['fig'][{key}] as {outnames['fig'][key]}")
+            dataset["fig"].savefig(outnames['fig'][key], overwrite=overwrite)
+            
     # save remaining keys as pickle files
     for key in dataset:
         if key not in outnames and key not in skip:
@@ -713,6 +721,7 @@ def run_proc_chain(
     overwrite=False,
     skip_save=None,
     extra_funcs=None,
+    covs=None,
     random_seed='auto',
     verbose="INFO",
     mneverbose="WARNING",
@@ -745,6 +754,8 @@ def run_proc_chain(
         List of keys to skip writing to disk. If None, we don't skip any keys.
     extra_funcs : list
         User-defined functions.
+    covs : dict, pd.DataFrame, or None
+        Covariates for GLM.
     random_seed : 'auto' (default), int or None
         Random seed to set. If 'auto', a random seed will be generated. Random seeds are set for both Python and NumPy.
         If None, no random seed is set.
@@ -857,6 +868,8 @@ def run_proc_chain(
             "epochs": None,
             "event_id": config["meta"]["event_codes"],
             "ica": None,
+            "covs": covs,
+            "fig": {},
         }
 
         # Do the preprocessing
@@ -864,6 +877,7 @@ def run_proc_chain(
             method, userargs = next(iter(stage.items()))
             target = userargs.get("target", "raw")  # Raw is default
             func = find_func(method, target=target, extra_funcs=extra_funcs)
+            
             # Actual function call
             dataset = func(dataset, userargs)
 
@@ -959,6 +973,7 @@ def run_proc_batch(
     overwrite=False,
     skip_save=None,
     extra_funcs=None,
+    covs=None,
     random_seed='auto',
     verbose="INFO",
     mneverbose="WARNING",
@@ -995,6 +1010,8 @@ def run_proc_batch(
         List of keys to skip writing to disk. If None, we don't skip any keys.    
     extra_funcs : list
         User-defined functions.
+    covs : dict or pd.DataFrame
+        Covariates to use for building the GLM design
     random_seed : 'auto' (default), int or None
         Random seed to set. If 'auto', a random seed will be generated. Random seeds are set for both Python and NumPy.
         If None, no random seed is set.
@@ -1102,6 +1119,7 @@ def run_proc_batch(
             overwrite=overwrite,
             skip_save=skip_save,
             extra_funcs=extra_funcs,
+            covs=covs,
             random_seed=random_seed,
         )
 
@@ -1153,11 +1171,19 @@ def run_proc_batch(
         for key in group_inputs[0]:
             dataset[key] = [group_inputs[i][key] for i in range(len(group_inputs))]
             skip_save.append(key)
+        
+        if covs is not None:
+            dataset['covs'] = covs
+        dataset['fig'] = {}
+        
         for stage in deepcopy(config["group"]):
             method, userargs = next(iter(stage.items()))
+            # make sure the function always knows it's a group processing
+            userargs['run_on_group'] = True
             target = userargs.get("target", "raw")  # Raw is default
             # skip.append(stage if userargs.get("skip_save") is True else None) # skip saving this stage to disk
             func = find_func(method, target=target, extra_funcs=extra_funcs)
+                
             # Actual function call
             dataset = func(dataset, userargs)
         outbase = os.path.join(outdir, "{ftype}.{fext}")
diff --git a/osl_ephys/preprocessing/osl_wrappers.py b/osl_ephys/preprocessing/osl_wrappers.py
index 175a600..f2f69a1 100644
--- a/osl_ephys/preprocessing/osl_wrappers.py
+++ b/osl_ephys/preprocessing/osl_wrappers.py
@@ -15,7 +15,9 @@
 from os.path import exists
 from scipy import stats
 from pathlib import Path
-
+import glmtools
+from ..glm import glm_epochs, glm_spectrum, glm_irasa, group_glm_epochs, group_glm_spectrum, MaxStatPermuteGLMSpectrum, ClusterPermuteGLMSpectrum
+from ..glm.glm_base import SensorMaxStatPerm, SensorClusterPerm
 logger = logging.getLogger(__name__)
 
 
@@ -922,3 +924,207 @@ def run_osl_ica_manualreject(dataset, userargs):
     else:
         logger.info("Components were not removed from raw data")
     return dataset
+
+#%% GLM wrappers
+
+def zscore_present_data(dataset, userargs):
+    """
+    z-scoring parametric regressors, without NaNs
+    Nans will be zeros in the z-scored version
+    
+    Parameters
+    ----------
+    dataset: dict
+        Dictionary containing at least an MNE object with the key ``covs``.
+    userargs: dict
+        Dictionary of additional arguments containing the keys ``keys``.
+    """
+    keys = userargs.pop("keys", None)
+    # make sure keys is a single string or list of strings
+    if keys[0]=='[' and keys[-1]==']':
+        keys = keys[1:-1].split(' ')
+        
+    for key in keys:
+        new = stats.zscore(dataset["covs"][key], nan_policy='omit')
+        new[np.isnan(dataset["covs"][key])] = 0
+        dataset["covs"][key] = new
+    return dataset
+
+
+def glm_add_regressor(dataset, userargs):
+    """osl-ephys Batch wrapper for :py:func:`osl_ephys.preprocessing.osl_glm.add_regressor <osl_ephys.preprocessing.osl_glm.add_regressor>`.
+
+    Parameters
+    """
+    logger.info("osl-ephys Stage - {0}".format("GLM Add Regressor"))
+    if 'design_config' not in dataset:
+        dataset['design_config'] = glmtools.design.DesignConfig()
+    
+    rtype = userargs.pop("rtype", None)
+    name = userargs.pop("name", None)
+    codes = userargs.pop("codes", None)
+    preproc = userargs.pop("preproc", None)
+    key = userargs.pop("key", None)
+    
+    if rtype == 'Constant':
+        dataset['design_config'].add_regressor(name, rtype)    
+    elif rtype == 'Categorical':
+        codes = [
+            float(codes)
+            if np.logical_or(type(codes) == int, type(codes) == float)
+            else np.array(codes.split(" ")).astype(float)
+            ]
+        dataset['design_config'].add_regressor(name, rtype, codes=codes)
+    elif rtype == 'Parametric':
+        dataset['design_config'].add_regressor(name, rtype, datainfo=key, preproc=preproc)
+    elif rtype == 'MeanEffects':
+        dataset['design_config'].add_regressor(name=name + '_{0}',rtype=rtype, datainfo=key)
+    else:
+        raise ValueError("Unknown regressor type")
+    return dataset
+
+
+def glm_add_contrast(dataset, userargs):
+    """osl-ephys Batch wrapper for :py:func:`osl_ephys.preprocessing.osl_glm.add_regressor <osl_ephys.preprocessing.osl_glm.add_regressor>`.
+
+    Parameters
+    """
+    logger.info("osl-ephys Stage - {0}".format("GLM Add Contrast"))
+    
+    simple = userargs.pop("simple", False)  
+    name = userargs.pop("name", None)
+    values = userargs.pop("values", None)
+    
+    if simple:
+        dataset['design_config'].add_simple_contrasts()
+    else:
+        import re
+        def string_to_dict(input_string):
+            # Replace unquoted keys with quoted keys
+            input_string = re.sub(r'(?<![\w])([a-zA-Z_][a-zA-Z0-9_]*)\s*:', r'"\1":', input_string)
+            # Evaluate the string as a dictionary
+            return eval(input_string)
+        values = string_to_dict(values)
+        dataset['design_config'].add_contrast(name=name, values=values)
+    
+    return dataset
+
+
+def glm(dataset, userargs):
+    """ wrapper for the different glm functions in the glm module
+    
+    Parameters
+    ----------
+    dataset: dict
+        Dictionary containing at least an MNE object with the key ``covs``.
+    userargs: dict
+        Dictionary of additional arguments
+        
+    Returns
+    -------
+    dataset: dict
+        Input dictionary containing MNE objects that have been modified in place.
+    """
+    run_on_group = userargs.pop("run_on_group", False)
+    target = userargs.pop("target", "raw")
+    name = userargs.pop("name", "glm")
+    method = userargs.pop("method", None)
+    if method is None:
+        raise ValueError("method not specified")
+    metric = userargs.pop("metric", 'copes')
+    
+    plot_summary = userargs.pop("plot_summary", True)
+    plot_efficiency = userargs.pop("plot_efficiency", True)
+    plot_leverage = userargs.pop("plot_leverage", True)
+    
+    if method == 'epochs' or method == 'glm_epochs':
+        baseline = userargs.pop("baseline", None)
+        if baseline is not None:
+            baseline = np.array(baseline[1:-1].split(" ")).astype(float)
+            
+        if run_on_group:
+            dataset[name] = group_glm_epochs(dataset[target], dataset['design_config'], dataset['covs'], metric, baseline)
+        else:
+            dataset[name] = glm_epochs(dataset['design_config'], dataset[target])
+    
+    elif method in ['spectrum', 'glm_spectrum', 'irasa', 'glm_irasa']:
+        if run_on_group:
+            dataset[name] = group_glm_spectrum(dataset[target], dataset['design_config'], dataset['covs'], metric, baseline)
+        else:
+            reg_categorical = userargs.pop("reg_categorical", None)
+            if reg_categorical[0]=='[' and reg_categorical[-1]==']':
+                reg_categorical = userargs["covs"][reg_categorical[1:-1].split(' ')]
+            else:
+                reg_categorical = userargs["covs"][reg_categorical]
+            
+            reg_ztrans = userargs.pop("reg_ztrans", None)
+            if reg_ztrans[0]=='[' and reg_ztrans[-1]==']':
+                reg_ztrans = userargs["covs"][reg_ztrans[1:-1].split(' ')]
+            else:
+                reg_ztrans = userargs["covs"][reg_ztrans]
+                
+            reg_unitmax = userargs.pop("reg_unitmax", None)
+            if reg_unitmax[0]=='[' and reg_unitmax[-1]==']':
+                reg_unitmax = userargs["covs"][reg_unitmax[1:-1].split(' ')]
+            else:
+                reg_unitmax = userargs["covs"][reg_unitmax]
+                
+            if method in ['spectrum', 'glm_spectrum']:
+                dataset[name] = glm_spectrum(dataset[target], reg_unitmax=reg_unitmax, reg_ztrans=reg_ztrans, reg_categorical=reg_categorical, **userargs)
+            else:
+                dataset[name] = glm_irasa(dataset[target], reg_unitmax=reg_unitmax, reg_ztrans=reg_ztrans, reg_categorical=reg_categorical, **userargs)
+                                               
+    if plot_summary:
+        dataset['fig'][name + 'design_summary'] = dataset[name].design.plot_summary(show=False)
+    
+    if plot_efficiency:
+        dataset['fig'][name + 'design_efficiency'] = dataset[name].design.plot_efficiency(show=False)
+        
+    if plot_leverage:
+        dataset['fig'][name + 'design_leverage'] = dataset[name].design.plot_leverage(show=False)
+
+    return dataset
+
+
+def glm_permutations(dataset, userargs):
+    """ wrapper for the different permutation options in the glm module
+    
+    Parameters
+    ----------
+    dataset: dict
+        Dictionary containing at least an MNE object with the key ``covs``.
+    userargs: dict
+        Dictionary of additional arguments
+        
+    Returns
+    -------
+    dataset: dict
+        Input dictionary containing MNE objects that have been modified in place.
+    """
+    target = userargs.pop("target", "glm")
+    name = userargs.pop("name", "glm_perm")
+    method = userargs.pop("method", None)
+    if method is None:
+        raise ValueError("method not specified")
+    type = userargs.pop("type", None)
+    if type is None:
+        raise ValueError("type not specified (e.g. 'max', 'cluster')")
+    
+    contrast = userargs.pop("contrast", None)
+    contrast = dataset[target].contrast_names.index(contrast)
+    fl_contrast = userargs.pop("fl_contrast", 0)
+    if fl_contrast != 0:
+        fl_contrast = dataset[target].fl_contrast_names.index(fl_contrast)
+    
+    if type in ['max', 'maxstat']:
+        if method == 'epochs' or method == 'glm_epochs':
+            dataset[name] = SensorMaxStatPerm(dataset[target], contrast, fl_contrast, **userargs)
+        elif method == 'spectrum' or method == 'glm_spectrum':
+            dataset[name] = MaxStatPermuteGLMSpectrum(dataset[target], contrast, fl_contrast, **userargs)
+    elif type == 'cluster':
+        if method == 'epochs' or method == 'glm_epochs':
+            dataset[name] = SensorClusterPerm(dataset[target], contrast, fl_contrast, **userargs)
+        elif method == 'spectrum' or method == 'glm_spectrum':
+            dataset[name] = ClusterPermuteGLMSpectrum(dataset[target], contrast, fl_contrast, **userargs)
+    
+    return dataset
\ No newline at end of file

From cbd44dce07249d752db3dada26b53d17cce20133 Mon Sep 17 00:00:00 2001
From: Mats <mats.vanes@psych.ox.ac.uk>
Date: Tue, 7 Jan 2025 15:37:54 +0000
Subject: [PATCH 02/10] add regressor option to glm wrapper

---
 osl_ephys/preprocessing/osl_wrappers.py | 27 ++++++++++++++++++-------
 1 file changed, 20 insertions(+), 7 deletions(-)

diff --git a/osl_ephys/preprocessing/osl_wrappers.py b/osl_ephys/preprocessing/osl_wrappers.py
index f2f69a1..5900b76 100644
--- a/osl_ephys/preprocessing/osl_wrappers.py
+++ b/osl_ephys/preprocessing/osl_wrappers.py
@@ -15,6 +15,7 @@
 from os.path import exists
 from scipy import stats
 from pathlib import Path
+import matplotlib.pyplot as plt
 import glmtools
 from ..glm import glm_epochs, glm_spectrum, glm_irasa, group_glm_epochs, group_glm_spectrum, MaxStatPermuteGLMSpectrum, ClusterPermuteGLMSpectrum
 from ..glm.glm_base import SensorMaxStatPerm, SensorClusterPerm
@@ -969,12 +970,17 @@ def glm_add_regressor(dataset, userargs):
     if rtype == 'Constant':
         dataset['design_config'].add_regressor(name, rtype)    
     elif rtype == 'Categorical':
-        codes = [
-            float(codes)
-            if np.logical_or(type(codes) == int, type(codes) == float)
-            else np.array(codes.split(" ")).astype(float)
-            ]
-        dataset['design_config'].add_regressor(name, rtype, codes=codes)
+        if codes == 'unique': # add a regressor for each unique value
+            codes = np.unique(dataset['covs'][key])
+            for code in codes:
+                dataset['design_config'].add_regressor(name + '_{0}'.format(code), rtype, codes=code)
+        else:
+            codes = [
+                float(codes)
+                if np.logical_or(type(codes) == int, type(codes) == float)
+                else np.array(codes.split(" ")).astype(float)
+                ]
+            dataset['design_config'].add_regressor(name, rtype, codes=codes)
     elif rtype == 'Parametric':
         dataset['design_config'].add_regressor(name, rtype, datainfo=key, preproc=preproc)
     elif rtype == 'MeanEffects':
@@ -1010,7 +1016,7 @@ def string_to_dict(input_string):
     return dataset
 
 
-def glm(dataset, userargs):
+def glm_fit(dataset, userargs):
     """ wrapper for the different glm functions in the glm module
     
     Parameters
@@ -1110,6 +1116,9 @@ def glm_permutations(dataset, userargs):
     if type is None:
         raise ValueError("type not specified (e.g. 'max', 'cluster')")
     
+    thresh = userargs.pop("thresh", 95)
+    plot_sig = userargs.pop("plot_sig", True)
+    
     contrast = userargs.pop("contrast", None)
     contrast = dataset[target].contrast_names.index(contrast)
     fl_contrast = userargs.pop("fl_contrast", 0)
@@ -1127,4 +1136,8 @@ def glm_permutations(dataset, userargs):
         elif method == 'spectrum' or method == 'glm_spectrum':
             dataset[name] = ClusterPermuteGLMSpectrum(dataset[target], contrast, fl_contrast, **userargs)
     
+    if plot_sig:
+        fig, ax = plt.subplots()
+        dataset[name].plot_sig_clusters(thresh, ax=ax)
+        dataset['fig'][name + 'sig' + thresh] = fig
     return dataset
\ No newline at end of file

From 8ba8cd63905c83c492ee3c40b402ffe3f05fe9ad Mon Sep 17 00:00:00 2001
From: Mats <mats.vanes@psych.ox.ac.uk>
Date: Tue, 7 Jan 2025 15:43:13 +0000
Subject: [PATCH 03/10] add glm_fit defaults

---
 osl_ephys/preprocessing/osl_wrappers.py | 25 ++++++++++++++++++++++---
 1 file changed, 22 insertions(+), 3 deletions(-)

diff --git a/osl_ephys/preprocessing/osl_wrappers.py b/osl_ephys/preprocessing/osl_wrappers.py
index 5900b76..c4ea177 100644
--- a/osl_ephys/preprocessing/osl_wrappers.py
+++ b/osl_ephys/preprocessing/osl_wrappers.py
@@ -954,8 +954,13 @@ def zscore_present_data(dataset, userargs):
 
 def glm_add_regressor(dataset, userargs):
     """osl-ephys Batch wrapper for :py:func:`osl_ephys.preprocessing.osl_glm.add_regressor <osl_ephys.preprocessing.osl_glm.add_regressor>`.
-
+    
     Parameters
+    ----------
+    dataset: dict
+        Dictionary containing at least an MNE object with the key ``covs``.
+    userargs: dict
+        Dictionary of additional arguments containing the keys ``keys``.
     """
     logger.info("osl-ephys Stage - {0}".format("GLM Add Regressor"))
     if 'design_config' not in dataset:
@@ -1032,11 +1037,25 @@ def glm_fit(dataset, userargs):
         Input dictionary containing MNE objects that have been modified in place.
     """
     run_on_group = userargs.pop("run_on_group", False)
-    target = userargs.pop("target", "raw")
-    name = userargs.pop("name", "glm")
+    
     method = userargs.pop("method", None)
     if method is None:
         raise ValueError("method not specified")
+    target = userargs.pop("target", None)
+    if target is None:
+        if run_on_group:
+            target = "glm"
+        else:
+            if method in ['epochs', 'glm_epochs']:
+                target = "epochs"
+            elif method in ['spectrum', 'glm_spectrum']:
+                target = "raw"
+    name = userargs.pop("name", None)
+    if name is None:
+        if run_on_group:
+            name = "group_glm"
+        else:
+            name = "glm"
     metric = userargs.pop("metric", 'copes')
     
     plot_summary = userargs.pop("plot_summary", True)

From cc44eac7cc88a045c0ef4735490285ee7ceaf900 Mon Sep 17 00:00:00 2001
From: Mats <mats.vanes@psych.ox.ac.uk>
Date: Tue, 7 Jan 2025 15:46:37 +0000
Subject: [PATCH 04/10] add glm perm defaults

---
 osl_ephys/preprocessing/osl_wrappers.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/osl_ephys/preprocessing/osl_wrappers.py b/osl_ephys/preprocessing/osl_wrappers.py
index c4ea177..d482b1a 100644
--- a/osl_ephys/preprocessing/osl_wrappers.py
+++ b/osl_ephys/preprocessing/osl_wrappers.py
@@ -1126,8 +1126,8 @@ def glm_permutations(dataset, userargs):
     dataset: dict
         Input dictionary containing MNE objects that have been modified in place.
     """
-    target = userargs.pop("target", "glm")
-    name = userargs.pop("name", "glm_perm")
+    target = userargs.pop("target", "group_glm")
+    name = userargs.pop("name", "group_glm_perm")
     method = userargs.pop("method", None)
     if method is None:
         raise ValueError("method not specified")
@@ -1135,7 +1135,7 @@ def glm_permutations(dataset, userargs):
     if type is None:
         raise ValueError("type not specified (e.g. 'max', 'cluster')")
     
-    thresh = userargs.pop("thresh", 95)
+    thresh = userargs.pop("threshold", 95)
     plot_sig = userargs.pop("plot_sig", True)
     
     contrast = userargs.pop("contrast", None)

From fb22e87a7b250093e92f38f3b2d626579c9dc39d Mon Sep 17 00:00:00 2001
From: Mats <mats.vanes@psych.ox.ac.uk>
Date: Tue, 7 Jan 2025 15:59:36 +0000
Subject: [PATCH 05/10] add glm contrast option

---
 osl_ephys/preprocessing/osl_wrappers.py | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/osl_ephys/preprocessing/osl_wrappers.py b/osl_ephys/preprocessing/osl_wrappers.py
index d482b1a..9494780 100644
--- a/osl_ephys/preprocessing/osl_wrappers.py
+++ b/osl_ephys/preprocessing/osl_wrappers.py
@@ -1009,13 +1009,17 @@ def glm_add_contrast(dataset, userargs):
     if simple:
         dataset['design_config'].add_simple_contrasts()
     else:
-        import re
-        def string_to_dict(input_string):
-            # Replace unquoted keys with quoted keys
-            input_string = re.sub(r'(?<![\w])([a-zA-Z_][a-zA-Z0-9_]*)\s*:', r'"\1":', input_string)
-            # Evaluate the string as a dictionary
-            return eval(input_string)
-        values = string_to_dict(values)
+        if values == 'unique':
+            values = np.unique(dataset['covs'][name])
+            values={f"{name}_{v}": 1/len(values) for v in values}
+        else:
+            import re
+            def string_to_dict(input_string):
+                # Replace unquoted keys with quoted keys
+                input_string = re.sub(r'(?<![\w])([a-zA-Z_][a-zA-Z0-9_]*)\s*:', r'"\1":', input_string)
+                # Evaluate the string as a dictionary
+                return eval(input_string)
+            values = string_to_dict(values)
         dataset['design_config'].add_contrast(name=name, values=values)
     
     return dataset

From a2f2f04661480d500383d20ff21c162e6dfe7af7 Mon Sep 17 00:00:00 2001
From: Mats <mats.vanes@psych.ox.ac.uk>
Date: Tue, 7 Jan 2025 16:11:20 +0000
Subject: [PATCH 06/10] remove covs input from proc_chain

---
 osl_ephys/preprocessing/batch.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/osl_ephys/preprocessing/batch.py b/osl_ephys/preprocessing/batch.py
index 61ab5f9..de108df 100644
--- a/osl_ephys/preprocessing/batch.py
+++ b/osl_ephys/preprocessing/batch.py
@@ -721,7 +721,6 @@ def run_proc_chain(
     overwrite=False,
     skip_save=None,
     extra_funcs=None,
-    covs=None,
     random_seed='auto',
     verbose="INFO",
     mneverbose="WARNING",
@@ -868,7 +867,6 @@ def run_proc_chain(
             "epochs": None,
             "event_id": config["meta"]["event_codes"],
             "ica": None,
-            "covs": covs,
             "fig": {},
         }
 

From dcfd22e729b795558494ff278e6baa6241394e67 Mon Sep 17 00:00:00 2001
From: Mats <mats.vanes@psych.ox.ac.uk>
Date: Tue, 7 Jan 2025 16:11:34 +0000
Subject: [PATCH 07/10] fix circular import

---
 osl_ephys/report/preproc_report.py | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/osl_ephys/report/preproc_report.py b/osl_ephys/report/preproc_report.py
index e978efe..afa4ecd 100644
--- a/osl_ephys/report/preproc_report.py
+++ b/osl_ephys/report/preproc_report.py
@@ -35,12 +35,6 @@
 
 from ..utils import process_file_inputs, validate_outdir
 from ..utils.logger import log_or_print
-from ..preprocessing import (
-    read_dataset,
-    load_config,
-    get_config_from_fif,
-    plot_preproc_flowchart,
-)
 
 
 # ----------------------------------------------------------------------------------
@@ -64,6 +58,7 @@ def gen_report_from_fif(infiles, outdir, ftype=None, logsdir=None, run_id=None):
     run_id : str
         Run ID.
     """
+    from ..preprocessing import read_dataset
 
     # Validate input files and directory to save html file and plots to
     infiles, outnames, good_files = process_file_inputs(infiles)
@@ -493,7 +488,7 @@ def plot_flowchart(raw, savebase=None):
         Path to saved figure.    
     
     """
-    
+    from ..preprocessing import get_config_from_fif, plot_preproc_flowchart
     # Get config info from raw.info['description']
     config_list = get_config_from_fif(raw)
 

From 54afaef1ab1e79feaae61d2201b126a7ec3f5fac Mon Sep 17 00:00:00 2001
From: Mats <mats.vanes@psych.ox.ac.uk>
Date: Tue, 7 Jan 2025 16:15:43 +0000
Subject: [PATCH 08/10] remove covs input from proc_chain

---
 osl_ephys/preprocessing/batch.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/osl_ephys/preprocessing/batch.py b/osl_ephys/preprocessing/batch.py
index de108df..e4c7eef 100644
--- a/osl_ephys/preprocessing/batch.py
+++ b/osl_ephys/preprocessing/batch.py
@@ -753,8 +753,6 @@ def run_proc_chain(
         List of keys to skip writing to disk. If None, we don't skip any keys.
     extra_funcs : list
         User-defined functions.
-    covs : dict, pd.DataFrame, or None
-        Covariates for GLM.
     random_seed : 'auto' (default), int or None
         Random seed to set. If 'auto', a random seed will be generated. Random seeds are set for both Python and NumPy.
         If None, no random seed is set.
@@ -1117,7 +1115,6 @@ def run_proc_batch(
             overwrite=overwrite,
             skip_save=skip_save,
             extra_funcs=extra_funcs,
-            covs=covs,
             random_seed=random_seed,
         )
 

From 3b44f96367bc3d2b49ecc6abbd728c802c61a51b Mon Sep 17 00:00:00 2001
From: Mats <mats.vanes@psych.ox.ac.uk>
Date: Tue, 7 Jan 2025 16:37:55 +0000
Subject: [PATCH 09/10] add run_osl to glm wrappers

---
 osl_ephys/preprocessing/osl_wrappers.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/osl_ephys/preprocessing/osl_wrappers.py b/osl_ephys/preprocessing/osl_wrappers.py
index 9494780..dc31397 100644
--- a/osl_ephys/preprocessing/osl_wrappers.py
+++ b/osl_ephys/preprocessing/osl_wrappers.py
@@ -928,7 +928,7 @@ def run_osl_ica_manualreject(dataset, userargs):
 
 #%% GLM wrappers
 
-def zscore_present_data(dataset, userargs):
+def run_osl_zscore_present_data(dataset, userargs):
     """
     z-scoring parametric regressors, without NaNs
     Nans will be zeros in the z-scored version
@@ -952,7 +952,7 @@ def zscore_present_data(dataset, userargs):
     return dataset
 
 
-def glm_add_regressor(dataset, userargs):
+def run_osl_glm_add_regressor(dataset, userargs):
     """osl-ephys Batch wrapper for :py:func:`osl_ephys.preprocessing.osl_glm.add_regressor <osl_ephys.preprocessing.osl_glm.add_regressor>`.
     
     Parameters
@@ -995,7 +995,7 @@ def glm_add_regressor(dataset, userargs):
     return dataset
 
 
-def glm_add_contrast(dataset, userargs):
+def run_osl_glm_add_contrast(dataset, userargs):
     """osl-ephys Batch wrapper for :py:func:`osl_ephys.preprocessing.osl_glm.add_regressor <osl_ephys.preprocessing.osl_glm.add_regressor>`.
 
     Parameters
@@ -1025,7 +1025,7 @@ def string_to_dict(input_string):
     return dataset
 
 
-def glm_fit(dataset, userargs):
+def run_osl_glm_fit(dataset, userargs):
     """ wrapper for the different glm functions in the glm module
     
     Parameters
@@ -1115,7 +1115,7 @@ def glm_fit(dataset, userargs):
     return dataset
 
 
-def glm_permutations(dataset, userargs):
+def run_osl_glm_permutations(dataset, userargs):
     """ wrapper for the different permutation options in the glm module
     
     Parameters

From 8739ab2a162a977436d18c4badc5e8f6157f55cf Mon Sep 17 00:00:00 2001
From: Mats <mats.vanes@psych.ox.ac.uk>
Date: Tue, 7 Jan 2025 18:09:18 +0000
Subject: [PATCH 10/10] glm wrapper bug fixes

---
 osl_ephys/preprocessing/batch.py        |  2 +-
 osl_ephys/preprocessing/osl_wrappers.py | 34 ++++++++++++-------------
 2 files changed, 17 insertions(+), 19 deletions(-)

diff --git a/osl_ephys/preprocessing/batch.py b/osl_ephys/preprocessing/batch.py
index e4c7eef..c180ee9 100644
--- a/osl_ephys/preprocessing/batch.py
+++ b/osl_ephys/preprocessing/batch.py
@@ -500,7 +500,7 @@ def write_dataset(dataset, outbase, run_id, ftype='preproc-raw', overwrite=False
         for key in keys:
             outnames['fig'][key] = outbase.format(run_id=run_id, ftype=key, fext="png")
             logger.info(f"Saving dataset['fig'][{key}] as {outnames['fig'][key]}")
-            dataset["fig"].savefig(outnames['fig'][key], overwrite=overwrite)
+            dataset["fig"][key].savefig(outnames['fig'][key])
             
     # save remaining keys as pickle files
     for key in dataset:
diff --git a/osl_ephys/preprocessing/osl_wrappers.py b/osl_ephys/preprocessing/osl_wrappers.py
index dc31397..2c1cc73 100644
--- a/osl_ephys/preprocessing/osl_wrappers.py
+++ b/osl_ephys/preprocessing/osl_wrappers.py
@@ -963,7 +963,7 @@ def run_osl_glm_add_regressor(dataset, userargs):
         Dictionary of additional arguments containing the keys ``keys``.
     """
     logger.info("osl-ephys Stage - {0}".format("GLM Add Regressor"))
-    if 'design_config' not in dataset:
+    if 'design_config' not in dataset or not isinstance(dataset['design_config'], glmtools.design.DesignConfig):
         dataset['design_config'] = glmtools.design.DesignConfig()
     
     rtype = userargs.pop("rtype", None)
@@ -978,16 +978,14 @@ def run_osl_glm_add_regressor(dataset, userargs):
         if codes == 'unique': # add a regressor for each unique value
             codes = np.unique(dataset['covs'][key])
             for code in codes:
-                dataset['design_config'].add_regressor(name + '_{0}'.format(code), rtype, codes=code)
+                dataset['design_config'].add_regressor(name=name + '_{0}'.format(code), rtype=rtype, codes=code)
         else:
-            codes = [
-                float(codes)
+            codes = [float(codes)
                 if np.logical_or(type(codes) == int, type(codes) == float)
-                else np.array(codes.split(" ")).astype(float)
-                ]
-            dataset['design_config'].add_regressor(name, rtype, codes=codes)
+                else np.array(codes[0].split(" ")).astype(float)][0]
+            dataset['design_config'].add_regressor(name=name, rtype=rtype, codes=codes)
     elif rtype == 'Parametric':
-        dataset['design_config'].add_regressor(name, rtype, datainfo=key, preproc=preproc)
+        dataset['design_config'].add_regressor(name=name, rtype=rtype, datainfo=key, preproc=preproc)
     elif rtype == 'MeanEffects':
         dataset['design_config'].add_regressor(name=name + '_{0}',rtype=rtype, datainfo=key)
     else:
@@ -1005,21 +1003,20 @@ def run_osl_glm_add_contrast(dataset, userargs):
     simple = userargs.pop("simple", False)  
     name = userargs.pop("name", None)
     values = userargs.pop("values", None)
+    key = userargs.pop("key", None)
     
     if simple:
         dataset['design_config'].add_simple_contrasts()
     else:
         if values == 'unique':
-            values = np.unique(dataset['covs'][name])
-            values={f"{name}_{v}": 1/len(values) for v in values}
+            values = np.unique(dataset['covs'][key])
+            values={f"{key}_{v}": 1/len(values) for v in values}
         else:
-            import re
-            def string_to_dict(input_string):
-                # Replace unquoted keys with quoted keys
-                input_string = re.sub(r'(?<![\w])([a-zA-Z_][a-zA-Z0-9_]*)\s*:', r'"\1":', input_string)
-                # Evaluate the string as a dictionary
-                return eval(input_string)
-            values = string_to_dict(values)
+            for key, value in values.items():
+                if isinstance(values[key], str):
+                    values[key] = float(eval(value))
+                else: 
+                    values[key] = float(value)
         dataset['design_config'].add_contrast(name=name, values=values)
     
     return dataset
@@ -1130,6 +1127,7 @@ def run_osl_glm_permutations(dataset, userargs):
     dataset: dict
         Input dictionary containing MNE objects that have been modified in place.
     """
+    run_on_group = userargs.pop("run_on_group", False)
     target = userargs.pop("target", "group_glm")
     name = userargs.pop("name", "group_glm_perm")
     method = userargs.pop("method", None)
@@ -1162,5 +1160,5 @@ def run_osl_glm_permutations(dataset, userargs):
     if plot_sig:
         fig, ax = plt.subplots()
         dataset[name].plot_sig_clusters(thresh, ax=ax)
-        dataset['fig'][name + 'sig' + thresh] = fig
+        dataset['fig'][name + 'sig' + str(thresh)] = fig
     return dataset
\ No newline at end of file