Merge pull request #84 from AGrigis/ag-extplugins2

External plugins mechanism

.travis.yml

@@ -59,10 +59,12 @@ install:
     - pip install sklearn
     - pip install nibabel
     - pip install progressbar2
-    - pip install astropy
+    - pip install astropy==2.0.8
     - pip install PyWavelets
-    - pip install git+https://github.com/CEA-COSMIC/ModOpt@master
-    - pip install -b $TRAVIS_BUILD_DIR/build -t $TRAVIS_BUILD_DIR/install --no-clean .
+    - pip install modopt
+    - pip install git+https://github.com/CEA-COSMIC/pysap-mri@master
+    - pip install git+https://github.com/CEA-COSMIC/pysap-astro@master
+    - pip install -b $TRAVIS_BUILD_DIR/build -t $TRAVIS_BUILD_DIR/install --no-clean --no-deps .
     - ls $TRAVIS_BUILD_DIR/install
     - ldd $TRAVIS_BUILD_DIR/install/pysparse.so
     - export PYTHONPATH=$TRAVIS_BUILD_DIR/install:$PYTHONPATH

examples/mri/cartesian_reconstruction.py

@@ -18,10 +18,10 @@
 # Package import
 import pysap
 from pysap.data import get_sample_data
-from pysap.numerics.reconstruct import sparse_rec_fista
-from pysap.numerics.reconstruct import sparse_rec_condatvu
-from pysap.numerics.utils import generate_operators
-from pysap.numerics.utils import convert_mask_to_locations
+from pysap.plugins.mri.numerics.reconstruct import sparse_rec_fista
+from pysap.plugins.mri.numerics.reconstruct import sparse_rec_condatvu
+from pysap.plugins.mri.numerics.utils import generate_operators
+from pysap.plugins.mri.numerics.utils import convert_mask_to_locations
 
 # Third party import
 import numpy as np

examples/mri/dictionary_learning_reconstruction.py

@@ -18,12 +18,12 @@
 # Package import
 import pysap
 from pysap.data import get_sample_data
-from pysap.numerics.fourier import FFT2
-from pysap.numerics.gradient import GradAnalysis2
-from pysap.numerics.reconstruct import sparse_rec_condatvu
-from pysap.numerics.proximity import Threshold
-from pysap.numerics.utils import convert_mask_to_locations
-from pysap.numerics.cost import DualGapCost
+from mri.numerics.fourier import FFT2
+from mri.numerics.gradient import GradAnalysis2
+from mri.numerics.reconstruct import sparse_rec_condatvu
+from mri.numerics.proximity import Threshold
+from mri.numerics.utils import convert_mask_to_locations
+from mri.numerics.cost import DualGapCost
 from pysap.plugins.mri.dictionary_learning.utils import learn_dictionary
 from pysap.plugins.mri.dictionary_learning.utils import min_max_normalize
 from pysap.plugins.mri.dictionary_learning.linear import DictionaryLearning

examples/mri/gridsearch.py

@@ -28,10 +28,10 @@
 
 # Package import
 from pysap.data import get_sample_data
-from pysap.numerics.gridsearch import grid_search
-from pysap.numerics.reconstruct import sparse_rec_condatvu
-from pysap.numerics.reconstruct import sparse_rec_fista
-from pysap.numerics.utils import convert_mask_to_locations
+from mri.numerics.gridsearch import grid_search
+from mri.numerics.reconstruct import sparse_rec_condatvu
+from mri.numerics.reconstruct import sparse_rec_fista
+from mri.numerics.utils import convert_mask_to_locations
 
 
 #############################################################################

examples/mri/non_cartesian_reconstruction.py

@@ -18,11 +18,11 @@
 # Package import
 import pysap
 from pysap.data import get_sample_data
-from pysap.numerics.fourier import NFFT
-from pysap.numerics.reconstruct import sparse_rec_fista
-from pysap.numerics.reconstruct import sparse_rec_condatvu
-from pysap.numerics.utils import generate_operators
-from pysap.numerics.utils import convert_mask_to_locations
+from mri.numerics.fourier import NFFT
+from mri.numerics.reconstruct import sparse_rec_fista
+from mri.numerics.reconstruct import sparse_rec_condatvu
+from mri.numerics.utils import generate_operators
+from mri.numerics.utils import convert_mask_to_locations
 
 # Third party import
 import numpy as np

examples/mri/p_mri_cartesian_reconstruction.py

@@ -11,14 +11,14 @@
 # Package import
 import pysap
 from pysap.data import get_sample_data
-from pysap.numerics.linear import Wavelet2
-from pysap.numerics.fourier import FFT2
-from pysap.numerics.reconstruct import sparse_rec_fista
-from pysap.numerics.reconstruct import sparse_rec_condatvu
-from pysap.numerics.utils import convert_mask_to_locations
-from pysap.numerics.utils import convert_locations_to_mask
-from pysap.numerics.gradient import Gradient_pMRI
-from pysap.numerics.proximity import Threshold
+from mri.numerics.linear import Wavelet2
+from mri.numerics.fourier import FFT2
+from mri.numerics.reconstruct import sparse_rec_fista
+from mri.numerics.reconstruct import sparse_rec_condatvu
+from mri.numerics.utils import convert_mask_to_locations
+from mri.numerics.utils import convert_locations_to_mask
+from mri.numerics.gradient import Gradient_pMRI
+from mri.numerics.proximity import Threshold
 
 # Third party import
 import numpy as np

examples/mri/p_mri_non_cartesian_reconstruction.py

@@ -11,12 +11,12 @@
 # Package import
 import pysap
 from pysap.data import get_sample_data
-from pysap.numerics.linear import Wavelet2
-from pysap.numerics.fourier import NFFT
-from pysap.numerics.reconstruct import sparse_rec_fista
-from pysap.numerics.reconstruct import sparse_rec_condatvu
-from pysap.numerics.gradient import Gradient_pMRI
-from pysap.numerics.proximity import Threshold
+from mri.numerics.linear import Wavelet2
+from mri.numerics.fourier import NFFT
+from mri.numerics.reconstruct import sparse_rec_fista
+from mri.numerics.reconstruct import sparse_rec_condatvu
+from mri.numerics.gradient import Gradient_pMRI
+from mri.numerics.proximity import Threshold
 from pysap.plugins.mri.parallel_mri.extract_sensitivity_maps import (
     extract_k_space_center_and_locations, get_Smaps)
 from pysap.plugins.mri.reconstruct.utils import normalize_frequency_locations

pysap/base/plugins.py

@@ -0,0 +1,81 @@
+# -*- coding: utf-8 -*-
+##########################################################################
+# pySAP - Copyright (C) CEA, 2017 - 2019
+# Distributed under the terms of the CeCILL-B license, as published by
+# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
+# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+# for details.
+##########################################################################
+
+# System import
+import sys
+import re
+import os
+import imp
+
+
+class PluginsMetaImportHook(object):
+    """ A class that import a module like normal except for the plugins that
+    monted on the pysap plugins module. The return value from the hack call
+    is put into sys.modules.
+    """
+    def __init__(self):
+        self.module = None
+
+    def find_module(self, name, path=None):
+        """ This method is called by Python if this class is on sys.path.
+        'name' is the fully-qualified name of the module to look for, and
+        'path' is either __path__ (for submodules and subpackages) or None (for
+        a top-level module/package).
+
+        Note that this method will be called every time an import statement
+        is detected (or __import__ is called), before Python's built-in
+        package/module-finding code kicks in.
+        """
+        # Use this loader only on registered modules
+        if re.match("pysap.plugins..*", name) is None:
+            return None
+        name = name.replace("pysap.plugins.", "")
+        if (len(name.split(".")) == 1):
+            path = None
+
+        # Get parent module and associated sub module names
+        self.sub_name = name.split(".")[-1]
+        self.mod_name = name.rpartition(".")[0]
+
+        # Find the sub module and build the module path
+        try:
+            self.file, self.filename, self.stuff = imp.find_module(
+                self.sub_name, path)
+            self.path = [self.filename]
+        except ImportError:
+            return None
+
+        # Return The loader, here the object itself
+        return self
+
+    def load_module(self, name):
+        """ This method is called by Python if PluginsMetaImportHook
+        'find_module' does not return None. 'name' is the fully-qualified name
+         of the module/package that was requested.
+        """
+        # Load the module
+        module = imp.load_module(name, self.file, self.filename,
+                                 self.stuff)
+        if self.file:
+            self.file.close()
+
+        # Update the module required information
+        module.__path__ = self.path
+        module.__loader__ = self
+        module.__package__ = name
+        module.__name__ = name
+        if self.stuff[0] == ".py":
+            module.__file__ = self.path[0]
+        else:
+            module.__file__ = os.path.join(self.path[0], "__init__.py")
+
+        return module
+
+
+sys.meta_path.insert(0, PluginsMetaImportHook())

pysap/configure.py

@@ -45,8 +45,9 @@ def _check_python_versions():
             raise ValueError("'{0}' dependency no formatted correctly.".format(
                 dependency))
         mod_name, mod_min_version = dependency.split(operator)
-        if mod_name == "progressbar2":
-            mod_name = "progressbar"
+        mod_name = mod_name.replace("pysap-", "")
+        if mod_name == "PyWavelets":
+            mod_name = "pywt"
         try:
             mod_install_version = importlib.import_module(mod_name).__version__
         except:

pysap/info.py

@@ -71,17 +71,20 @@
 VERSION = __version__
 PROVIDES = ["pysap"]
 REQUIRES = [
-    "scipy>=1.0.0",
+    "scipy>=0.18.0",
     "numpy>=1.11.0",
-    "matplotlib>=2.1.2",
+    "matplotlib>=2.0.0",
     "future>=0.16.0",
     "astropy==2.0.8",
     "nibabel>=2.1.0",
     "pyqtgraph>=0.10.0",
-    "progressbar2>=3.34.3",
-    "modopt>=1.1.5",
-    "scikit-learn>=0.19.1",
-    "PyWavelets>=1.0.0"
+    "PyWavelets>=1.0.0",
+    "pysap-mri==0.0.0",
+    "pysap-astro==0.0.0"
+]
+DEPENDENCY_LINKS = [
+    "git+https://github.com/CEA-COSMIC/pysap-mri.git#egg=pysap-mri-0.0.0",
+    "git+https://github.com/CEA-COSMIC/pysap-astro.git#egg=pysap-astro-0.0.0",
 ]
 EXTRA_REQUIRES = {
     "gui": {