From 363f9e0bb482ae30afa9db0936b65f4729a93afd Mon Sep 17 00:00:00 2001 From: LeSasse Date: Mon, 20 Mar 2023 16:46:17 +0100 Subject: [PATCH 1/6] add extra input parameter to abstract aggregate method in fc base --- .../functional_connectivity_base.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/junifer/markers/functional_connectivity/functional_connectivity_base.py b/junifer/markers/functional_connectivity/functional_connectivity_base.py index dbabe6bd1..72f7ad135 100644 --- a/junifer/markers/functional_connectivity/functional_connectivity_base.py +++ b/junifer/markers/functional_connectivity/functional_connectivity_base.py @@ -66,7 +66,11 @@ class FunctionalConnectivityBase(BaseMarker): super().__init__(on="BOLD", name=name) @abstractmethod - def aggregate(self, input: Dict[str, Any]) -> Dict[str, Any]: + def aggregate( + self, + input: Dict[str, Any], + extra_input: Optional[Dict[str, Any]] = None, + ) -> Dict[str, Any]: """Perform aggregation.""" raise_error( msg="Concrete classes need to implement aggregate().", @@ -130,7 +134,7 @@ class FunctionalConnectivityBase(BaseMarker): """ # Perform necessary aggregation - aggregation = self.aggregate(input) + aggregation = self.aggregate(input, extra_input=extra_input) # Compute correlation if self.cor_method_params["empirical"]: connectivity = ConnectivityMeasure( -- 2.52.0 From 2ada151ec66297663fe4b2a868af7bb47371c7da Mon Sep 17 00:00:00 2001 From: LeSasse Date: Mon, 20 Mar 2023 16:49:51 +0100 Subject: [PATCH 2/6] add entry to latest.inc --- docs/changes/latest.inc | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index f7e833622..2b107e85c 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -81,6 +81,8 @@ Bugs - Fix a bug in which :class:`junifer.markers.ParcelAggregation` could yield duplicated column names if two or more parcels were used and label names were not unique (:gh:`194` by `Fede Raimondo`_). +- Fix a bug in which :func:`get_masks` fails for :class:`FunctionalConnectivityBase` because of missing extra_input parameter + API changes ~~~~~~~~~~~ -- 2.52.0 From e2bfe3d6a27158cb74f03c74137202b0fde8731a Mon Sep 17 00:00:00 2001 From: LeSasse Date: Mon, 20 Mar 2023 17:06:26 +0100 Subject: [PATCH 3/6] fix entry to latest.inc? --- docs/changes/latest.inc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index 2b107e85c..5f8e7c331 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -81,7 +81,7 @@ Bugs - Fix a bug in which :class:`junifer.markers.ParcelAggregation` could yield duplicated column names if two or more parcels were used and label names were not unique (:gh:`194` by `Fede Raimondo`_). -- Fix a bug in which :func:`get_masks` fails for :class:`FunctionalConnectivityBase` because of missing extra_input parameter +- Fix a bug in which :func:`junifer.data.masks.get_masks` fails for :class:`junifer.markers.functional_connectivity_base.FunctionalConnectivityBase` because of missing extra_input parameter (by `Leonard Sasse`_) API changes ~~~~~~~~~~~ -- 2.52.0 From 2f68b4525d3d6100b39b8811bfbc62ab34dae6a3 Mon Sep 17 00:00:00 2001 From: LeSasse Date: Mon, 20 Mar 2023 17:10:29 +0100 Subject: [PATCH 4/6] fix entry to latest.inc? this time really --- docs/changes/latest.inc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index 5f8e7c331..be4702321 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -81,7 +81,7 @@ Bugs - Fix a bug in which :class:`junifer.markers.ParcelAggregation` could yield duplicated column names if two or more parcels were used and label names were not unique (:gh:`194` by `Fede Raimondo`_). -- Fix a bug in which :func:`junifer.data.masks.get_masks` fails for :class:`junifer.markers.functional_connectivity_base.FunctionalConnectivityBase` because of missing extra_input parameter (by `Leonard Sasse`_) +- Fix a bug in which :func:`junifer.data.masks.get_masks` fails for :class:`junifer.markers.functional_connectivity_base.FunctionalConnectivityBase` because of missing extra_input parameter (:gh:`200` by `Leonard Sasse`_) API changes ~~~~~~~~~~~ -- 2.52.0 From f8b35b0571abb609675f7224de8f5b9d98d2e21e Mon Sep 17 00:00:00 2001 From: LeSasse Date: Mon, 20 Mar 2023 17:22:58 +0100 Subject: [PATCH 5/6] fix entry to latest.inc? this time really really --- docs/changes/latest.inc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index be4702321..f5f3e2857 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -81,7 +81,7 @@ Bugs - Fix a bug in which :class:`junifer.markers.ParcelAggregation` could yield duplicated column names if two or more parcels were used and label names were not unique (:gh:`194` by `Fede Raimondo`_). -- Fix a bug in which :func:`junifer.data.masks.get_masks` fails for :class:`junifer.markers.functional_connectivity_base.FunctionalConnectivityBase` because of missing extra_input parameter (:gh:`200` by `Leonard Sasse`_) +- Fix a bug in which :func:`junifer.data.masks.get_mask` fails for :class:`junifer.markers.functional_connectivity.functional_connectivity_base.FunctionalConnectivityBase` because of missing extra_input parameter (:gh:`200` by `Leonard Sasse`_) API changes ~~~~~~~~~~~ -- 2.52.0 From b10e4eb6d755684ae981f09eaf355497906ac0bb Mon Sep 17 00:00:00 2001 From: LeSasse Date: Mon, 20 Mar 2023 17:32:38 +0100 Subject: [PATCH 6/6] Fix latest.inc! --- docs/changes/latest.inc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index f5f3e2857..2c5e7267f 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -81,7 +81,7 @@ Bugs - Fix a bug in which :class:`junifer.markers.ParcelAggregation` could yield duplicated column names if two or more parcels were used and label names were not unique (:gh:`194` by `Fede Raimondo`_). -- Fix a bug in which :func:`junifer.data.masks.get_mask` fails for :class:`junifer.markers.functional_connectivity.functional_connectivity_base.FunctionalConnectivityBase` because of missing extra_input parameter (:gh:`200` by `Leonard Sasse`_) +- Fix a bug in which :func:`junifer.data.masks.get_mask` fails for FunctionalConnectivityBase class, because of missing extra_input parameter (:gh:`200` by `Leonard Sasse`_) API changes ~~~~~~~~~~~ -- 2.52.0