Merge pull request #125 from BrainLesion/retire_ereg

cleaning ereg

Author: neuronflow

README.md

@@ -121,7 +121,7 @@ We provide a (WIP) documentation. Have a look [here](https://brainles-preprocess
 Please credit the authors by citing their work.
 
 ### Registration
-We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default), [Niftyreg](https://github.com/KCL-BMEIS/niftyreg) (Linux), eReg (experimental)
+We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default), [Niftyreg](https://github.com/KCL-BMEIS/niftyreg) (Linux).
 
 ### Atlas Reference
 We provide the SRI-24 atlas from this [publication](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915788/).

brainles_preprocessing/registration/__init__.py

@@ -8,13 +8,6 @@
         "ANTS package not found. If you want to use it, please install it using 'pip install antspyx'"
     )
 
-try:
-    from .eReg.eReg import eRegRegistrator
-except ImportError:
-    warnings.warn(
-        "eReg package not found. If you want to use it, please install it using 'pip install brainles_preprocessing[ereg]'"
-    )
-
 
 from .niftyreg.niftyreg import NiftyRegRegistrator
 

brainles_preprocessing/registration/eReg/__init__.py

@@ -14,12 +14,6 @@ registration.ANTs
 .. automodule:: brainles_preprocessing.registration.ANTs.ANTs
 
 
-registration.eReg
---------------------------------------
-
-.. automodule:: brainles_preprocessing.registration.eReg.eReg
-
-
 registration.niftyreg
 --------------------------------------
 

brainles_preprocessing/registration/eReg/config_files/TODO.md

@@ -11,7 +11,6 @@
 from brainles_preprocessing.registration import (
     ANTsRegistrator,
     # NiftyRegRegistrator,
-    # eRegRegistrator,
 )
 
 
@@ -127,7 +126,6 @@ def preprocess(inputDir):
             # choose the registration backend you want to use
             # registrator=NiftyRegRegistrator(),
             registrator=ANTsRegistrator(),
-            # registrator=eRegRegistrator(),
             brain_extractor=HDBetExtractor(),
             temp_folder="temporary_directory",
             limit_cuda_visible_devices="0",

brainles_preprocessing/registration/eReg/eReg.py

@@ -69,14 +69,12 @@ auxiliary = ">=0.0.42"
 rich = "^13.6.0"
 
 # optional registration backends
-ereg = { version = "^0.0.10", optional = true }
 itk-elastix = { version = "^0.20.0", optional = true }
 picsl_greedy = { version = "^0.0.6", optional = true }
 
 
 [tool.poetry.extras]
-all = ["ereg", "itk-elastix", "picsl_greedy"]
-ereg = ["ereg"]
+all = ["itk-elastix", "picsl_greedy"]
 itk-elastix = ["itk-elastix"]
 picsl_greedy = ["picsl_greedy"]
 

docs/source/registration.rst

@@ -1,7 +1,6 @@
 from registrator_base import RegistratorBase
 
 from brainles_preprocessing.registration.ANTs.ANTs import ANTsRegistrator
-from brainles_preprocessing.registration.eReg.eReg import eRegRegistrator
 from brainles_preprocessing.registration.niftyreg.niftyreg import NiftyRegRegistrator
 from brainles_preprocessing.registration.elastix.elastix import ElastixRegistrator
 from brainles_preprocessing.registration.greedy.greedy import GreedyRegistrator
@@ -25,14 +24,6 @@ def get_method_and_extension(self):
         return "niftyreg", "txt"
 
 
-class TestEregRegistrator(RegistratorBase, unittest.TestCase):
-    def get_registrator(self):
-        return eRegRegistrator()
-
-    def get_method_and_extension(self):
-        return "ereg", "mat"
-
-
 class TestElastixRegistrator(RegistratorBase, unittest.TestCase):
     def get_registrator(self):
         return ElastixRegistrator()