Rename mia_processes/python/mia_processes to mia_processes/mia_processe

Author: servoz

.idea/mia_processes.iml

@@ -15,7 +15,7 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath("../../python"))
+sys.path.insert(0, os.path.abspath("../../"))
 # Next lines to use only in dev mode (not when pushing to github)
 sys.path.insert(0, os.path.abspath("../../../populse_mia/python"))
 sys.path.insert(0, os.path.abspath("../../../populse_db/python"))

docs/source/conf.py

@@ -0,0 +1,23 @@
+# -*- coding: utf-8 -*-
+"""
+Mia_processes is the official bricks library for populse_mia.
+A brick can be an atomic operation or a pipeline (a succession of atomic
+calculations).
+
+:Contains:
+    :Packages:
+        - bricks: the library of atomic bricks
+        - pipelines: the pipelines library
+        - utils: various general tools used in bricks or pipelines
+
+"""
+
+##########################################################################
+# mia_processes - Copyright (C) IRMaGe/CEA, 2018
+# Distributed under the terms of the CeCILL license, as published by
+# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
+# http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html
+# for details.
+##########################################################################
+
+from .info import __version__  # noqa: F401

mia_processes/__init__.py

@@ -0,0 +1,18 @@
+# -*- coding: utf-8 -*-
+"""
+:Contains:
+    :Packages:
+        - preprocess: bricks used in the pre-treatment stage
+        - reports: bricks used in the reports generation
+        - stat: bricks used in the statistical calculation stage
+        - tools: various bricks used as tools
+
+"""
+
+##########################################################################
+# mia_processes - Copyright (C) IRMaGe/CEA, 2018
+# Distributed under the terms of the CeCILL license, as published by
+# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
+# http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html
+# for details.
+##########################################################################

mia_processes/bricks/__init__.py

@@ -0,0 +1,23 @@
+# -*- coding: utf-8 -*-
+"""
+Each package corresponds to a software encapsulated in mia_processes.
+
+:Contains:
+    :Packages:
+        - afni: bricks from afni
+        - ants: bricks from ants
+        - dipy: bricks from dipy
+        - freesurfer: bricks from freesurfer
+        - fsl: bricks from fsl
+        - other: bricks from other sources (usually home made bricks)
+        - spm: bricks from spm
+
+"""
+
+##########################################################################
+# mia_processes - Copyright (C) IRMaGe/CEA, 2018
+# Distributed under the terms of the CeCILL license, as published by
+# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
+# http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html
+# for details.
+##########################################################################

mia_processes/bricks/preprocess/__init__.py

@@ -0,0 +1,29 @@
+# -*- coding: utf-8 -*-
+"""
+The atomic calculations from afni.
+
+"""
+
+##########################################################################
+# mia_processes - Copyright (C) IRMaGe/CEA, 2018
+# Distributed under the terms of the CeCILL license, as published by
+# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
+# http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html
+# for details.
+##########################################################################
+
+from .processes import (  # noqa: F401
+    GCOR,
+    Automask,
+    Calc,
+    CalcDropTRs,
+    Despike,
+    FWHMx,
+    OutlierCount,
+    QualityIndex,
+    RefitDeoblique,
+    SkullStrip,
+    TShift,
+    TStatMean,
+    Volreg,
+)