eegprep 0.1.1__tar.gz → 0.2.3__tar.gz

{eegprep-0.1.1/src/eegprep.egg-info → eegprep-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegprep
-Version: 0.1.1
+Version: 0.2.3
 Summary: EEG preprocessing pipeline on Python
 Author-email: Arnaud Delorme <adelorme@gmail.com>, Young Truong <dt.young112@gmail.com>
 License: BSD 2-Clause License
@@ -55,6 +55,7 @@ Requires-Dist: python-picard<0.9,>=0.8
 Requires-Dist: scipy>=1.7.0
 Requires-Dist: sympy>=1.14.0
 Requires-Dist: threadpoolctl>=3.6.0
+Requires-Dist: torch
 Provides-Extra: torch
 Requires-Dist: torch>=1.10.0; extra == "torch"
 Provides-Extra: eeglabio
@@ -99,15 +100,17 @@ The MATLAB and Python implementations were compared using the first two subjects
 
 ## Build Docker
 
-```
-docker run --rm -it -v $(pwd):/usr/src/project dtyoung/eegprep /bin/bash
-docker run -u root --rm -it -v $(pwd):/usr/src/project dtyoung/eegprep /bin/bash
-```
-
-## Remove Docker
+### versioning
+- pyproject version (change version inside file)
+- main version (change version inside file)
+- git tag
+- docker version when building (see below)
 
+### building
 ```
-docker rmi dtyoung/eegprep
+docker build -t eegprep:0.2.3 -f DOCKERFILE .
+docker tag eegprep:0.2.1 arnodelorme/eegprep:0.2.3
+docker push arnodelorme/eegprep:0.2.3  
 ```
 
 Mounted folder in /usr/src/project

{eegprep-0.1.1 → eegprep-0.2.3}/README.md

@@ -33,15 +33,17 @@ The MATLAB and Python implementations were compared using the first two subjects
 
 ## Build Docker
 
-```
-docker run --rm -it -v $(pwd):/usr/src/project dtyoung/eegprep /bin/bash
-docker run -u root --rm -it -v $(pwd):/usr/src/project dtyoung/eegprep /bin/bash
-```
-
-## Remove Docker
+### versioning
+- pyproject version (change version inside file)
+- main version (change version inside file)
+- git tag
+- docker version when building (see below)
 
+### building
 ```
-docker rmi dtyoung/eegprep
+docker build -t eegprep:0.2.3 -f DOCKERFILE .
+docker tag eegprep:0.2.1 arnodelorme/eegprep:0.2.3
+docker push arnodelorme/eegprep:0.2.3  
 ```
 
 Mounted folder in /usr/src/project

{eegprep-0.1.1 → eegprep-0.2.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "eegprep"
-version = "0.1.1"
+version = "0.2.3"
 authors = [
   { name="Arnaud Delorme", email="adelorme@gmail.com" },
   { name="Young Truong", email="dt.young112@gmail.com" },
@@ -37,6 +37,7 @@ dependencies = [
   "scipy>=1.7.0",
   "sympy>=1.14.0",
   "threadpoolctl>=3.6.0",
+  "torch"
 ]
 
 [project.optional-dependencies]
@@ -52,7 +53,7 @@ all = [
 ]
 
 [tool.setuptools]
-include-package-data = false
+include-package-data = true
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -62,7 +63,8 @@ exclude = ["eegprep.eeglab*"]
 "eegprep" = [
   "resources/montages/*.locs",
   "resources/montages/README.md",
-  "resources/*.m"
+  "resources/*.m",
+  "netICL.mat"
 ]
 
 [tool.setuptools.exclude-package-data]

{eegprep-0.1.1 → eegprep-0.2.3}/src/eegprep/ICL_feature_extractor.py

@@ -36,7 +36,8 @@ def ICL_feature_extractor(EEG, flag_autocorr=False):
     # Calculate topo
     topo = np.zeros((32, 32, 1, ncomp))
     for it in range(ncomp):
-        _, temp_topo, _, _, _ = topoplot(EEG['icawinv'][:, it], EEG['chanlocs'][EEG['icachansind']], noplot='on')
+        tmp_chanlocs = [EEG['chanlocs'][i] for i in EEG['icachansind']]
+        _, temp_topo, _, _, _ = topoplot(EEG['icawinv'][:, it], tmp_chanlocs, noplot='on')
         temp_topo[np.isnan(temp_topo)] = 0
         topo[:, :, 0, it] = temp_topo / np.max(np.abs(temp_topo))
 

{eegprep-0.1.1 → eegprep-0.2.3}/src/eegprep/clean_artifacts.py

@@ -32,7 +32,7 @@ def clean_artifacts(
     ChannelCriterionMaxBadTime: float = 0.5,
     BurstCriterionRefMaxBadChns: Union[float, str, None] = 0.075,
     BurstCriterionRefTolerances: Union[Tuple[float, float], str, None] = (-np.inf, 5.5),
-    BurstRejection: str = 'off',
+    BurstRejection: bool = False,
     WindowCriterionTolerances: Union[Tuple[float, float], str, None] = (-np.inf, 7),
     FlatlineCriterion: Union[float, str, None] = 5.0,
     NumSamples: int = 50,
@@ -250,7 +250,7 @@ def clean_artifacts(
                 maxmem=int(MaxMem),
             )
 
-        if BurstRejection.lower() == 'on':
+        if BurstRejection:
             # Determine unchanged samples after ASR repair
             sample_mask = np.sum(np.abs(EEG['data'] - BUR['data']), axis=0) < 1e-8
             # Convert to intervals (start,end) inclusive

{eegprep-0.1.1 → eegprep-0.2.3/src/eegprep.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegprep
-Version: 0.1.1
+Version: 0.2.3
 Summary: EEG preprocessing pipeline on Python
 Author-email: Arnaud Delorme <adelorme@gmail.com>, Young Truong <dt.young112@gmail.com>
 License: BSD 2-Clause License
@@ -55,6 +55,7 @@ Requires-Dist: python-picard<0.9,>=0.8
 Requires-Dist: scipy>=1.7.0
 Requires-Dist: sympy>=1.14.0
 Requires-Dist: threadpoolctl>=3.6.0
+Requires-Dist: torch
 Provides-Extra: torch
 Requires-Dist: torch>=1.10.0; extra == "torch"
 Provides-Extra: eeglabio
@@ -99,15 +100,17 @@ The MATLAB and Python implementations were compared using the first two subjects
 
 ## Build Docker
 
-```
-docker run --rm -it -v $(pwd):/usr/src/project dtyoung/eegprep /bin/bash
-docker run -u root --rm -it -v $(pwd):/usr/src/project dtyoung/eegprep /bin/bash
-```
-
-## Remove Docker
+### versioning
+- pyproject version (change version inside file)
+- main version (change version inside file)
+- git tag
+- docker version when building (see below)
 
+### building
 ```
-docker rmi dtyoung/eegprep
+docker build -t eegprep:0.2.3 -f DOCKERFILE .
+docker tag eegprep:0.2.1 arnodelorme/eegprep:0.2.3
+docker push arnodelorme/eegprep:0.2.3  
 ```
 
 Mounted folder in /usr/src/project

{eegprep-0.1.1 → eegprep-0.2.3}/src/eegprep.egg-info/SOURCES.txt

@@ -36,6 +36,7 @@ src/eegprep/epoch.py
 src/eegprep/iclabel.py
 src/eegprep/iclabel_net.py
 src/eegprep/iclabel_net_load_py_measures.py
+src/eegprep/netICL.mat
 src/eegprep/pinv.py
 src/eegprep/pop_epoch.py
 src/eegprep/pop_load_frombids.py

{eegprep-0.1.1 → eegprep-0.2.3}/src/eegprep.egg-info/requires.txt

@@ -12,6 +12,7 @@ python-picard<0.9,>=0.8
 scipy>=1.7.0
 sympy>=1.14.0
 threadpoolctl>=3.6.0
+torch
 
 [all]
 torch>=1.10.0