Fixed outport bug, add tomography module and update to latest VTTools

Merge remote-tracking branch 'upstream/master'

conda-recipe/build.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+$PYTHON setup.py install
+cp -r vt_config/NSLS-II $SP_DIR/vistrails/packages/

conda-recipe/meta.yaml

@@ -0,0 +1,33 @@
+package:
+  name: vttools
+  version: {{ environ['GIT_DESCRIBE_TAG'] }}.post{{ environ['GIT_DESCRIBE_NUMBER'] }}
+
+source:
+  git_url: ../
+
+
+build:
+  number: 0
+  string: {{ environ.get('GIT_BUILD_STR', '') }}_np{{ np }}py{{ py }}
+
+requirements:
+  build:
+    - python
+    - setuptools
+    - vistrails
+  run:
+    - python
+    - vistrails
+    - numpy
+    - scikit-xray
+    - pyyaml
+    - numpydoc
+    - tifffile
+    - bubblegum
+
+test:
+  imports:
+     - vttools
+
+about:
+  license: 3-Clause BSD

setup.py

@@ -1,31 +1,15 @@
-#!/usr/bin/env python
 
 import setuptools
-from distutils.core import setup, Extension
-
-import numpy as np
-import os
-import shutil
-from subprocess import call
-import sys
+from distutils.core import setup
 
 setup(
     name='vttools',
     version='0.0.x',
     author='Brookhaven National Lab',
     packages=["vttools",
               'vttools.vtmods',
-              'vttools.vtmods.import_lists'
+              'vttools.vtmods.import_lists',
+              'vttools.to_wrap'
               ],
-    include_dirs=[np.get_include()],
     package_data = {'vttools.vtmods.import_lists': ['*.yaml']}
     )
-
-
-src = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'vt_config',
-                   'NSLS-II')
-dst = os.path.join(os.path.expanduser('~'), '.vistrails', 'userpackages',
-                   'NSLS-II')
-
-from vttools.utils import make_symlink
-make_symlink(dst=dst, src=src)

vt_config/NSLS-II/init.py

@@ -36,7 +36,7 @@
 Created on Apr 29, 2014
 '''
 from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+                        )
 import six
 import logging
 import sys

vttools/__init__.py

@@ -34,7 +34,7 @@
 ########################################################################
 
 from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+                        )
 
 import six
 import logging

vttools/func_wrap_smoketest.py

@@ -36,7 +36,7 @@
 This module is for spectroscopy specific tools (spectrum fitting etc).
 """
 from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+                        )
 
 import six
 from six.moves import zip

vttools/tests/test_fitting.py

@@ -33,7 +33,7 @@
 # POSSIBILITY OF SUCH DAMAGE.                                          #
 ########################################################################
 from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+                        )
 
 import numpy as np
 import six
@@ -43,7 +43,7 @@
 from skxray.testing.decorators import known_fail_if
 from vttools.to_wrap.fitting import (gaussian_model, lorentzian_model,
                                      lorentzian2_model, quadratic_model,
-                                     fit_engine)
+                                     fit_engine, fit_engine_list, expression_model)
 from nose.tools import (assert_equal, assert_true, raises)
 
 
@@ -114,6 +114,7 @@ def test_lorentzian2_fit():
     fitted_val = (out['area'], out['center'], out['sigma'])
     assert_array_almost_equal(true_val, fitted_val)
 
+
 def test_quadratic_fit():
     x = np.arange(-1, 1, .01)
     a = 1
@@ -133,3 +134,31 @@ def test_quadratic_fit():
     out = result.values
     fitted_val = (out['a'], out['b'], out['c'])
     assert_array_almost_equal(true_val, fitted_val)
+
+
+def test_fit_engine_list():
+    a = 1
+    b = 2
+    c = 3
+    m = quadratic_model('',
+                        a, 'free', [-1, 1],
+                        b, 'free', [-1, 1],
+                        c, 'free', [-1, 1])
+    x = np.arange(-1, 1, 0.01)
+    y = x**2 + 1
+
+    datav = [(x, y), (x, y+2)]
+    out = fit_engine_list(m, datav)
+    assert_equal(len(out), 2)
+
+
+def test_expression_model():
+
+    inputv = 'exp(-a*x)'
+
+    x = np.arange(-1, 1, 0.01)
+    y = np.exp(-x)
+
+    mod = expression_model(inputv)
+    out = mod.fit(y, x=x, a=0.1)
+    assert_equal(1, out.values['a'])

vttools/tests/test_wrap_lib.py

@@ -34,7 +34,7 @@
 ########################################################################
 
 from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+                        )
 
 import six
 import logging

vttools/to_wrap/fitting.py

@@ -34,7 +34,8 @@
 ########################################################################
 import sys
 from skxray.fitting.api import (QuadraticModel, GaussianModel,
-                                 LorentzianModel, Lorentzian2Model)
+                                LorentzianModel, Lorentzian2Model,
+                                ExpressionModel)
 
 import logging
 logger = logging.getLogger(__name__)
@@ -150,6 +151,24 @@ def fit_engine_list(g, data):
     return result_list
 
 
+def expression_model(model_exp):
+    """
+    This function creates a Model from a user-supplied expression.
+
+    Parameters
+    ----------
+    model_exp : str
+        expression of the model
+
+    Returns
+    -------
+    mod : array_like
+        object of fitting results
+    """
+    mod = ExpressionModel(model_exp)
+    return mod
+
+
 def set_range(model_name,
               parameter_name, parameter_value,
               parameter_vary, parameter_range):
@@ -265,9 +284,3 @@ def inner(prefix, amplitude, amplitude_vary, amplitude_range,
     func_name.amplitude_vary = ['fixed', 'free', 'bounded']
     func_name.center_vary = ['fixed', 'free', 'bounded']
     func_name.sigma_vary = ['fixed', 'free', 'bounded']
-
-
-function_list = [fit_engine, fit_engine_list, quadratic_model]
-
-for func_name in function_list:
-    setattr(mod, func_name.__name__, func_name)

vttools/utils.py

@@ -34,7 +34,7 @@
 ########################################################################
 
 from __future__ import (absolute_import, division,
-                        print_function, unicode_literals)
+                        print_function, )
 import six
 import os
 import shutil

vttools/vtmods/broker.py

@@ -36,7 +36,7 @@
 Created on Apr 29, 2014
 '''
 from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+                        )
 import six
 from PyQt4 import QtCore, QtGui
 from vistrails.core.modules.vistrails_module import Module, ModuleSettings

vttools/vtmods/fitting.py

@@ -34,7 +34,7 @@
 ########################################################################
 
 from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+                        )
 import six
 from vistrails.core.modules.vistrails_module import Module, ModuleSettings
 from vistrails.core.modules.config import IPort, OPort

vttools/vtmods/import_lists/__init__.py

@@ -34,7 +34,7 @@
 ########################################################################
 
 from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+                        )
 import six
 import os
 import yaml

vttools/vtmods/import_lists/modules.yaml

@@ -74,6 +74,9 @@ autowrap_func:
 - func_name: fit_engine_list
   module_path: vttools.to_wrap.fitting
   namespace: fitting
+- func_name: expression_model
+  module_path: vttools.to_wrap.fitting
+  namespace: fitting
 # CALIBRATION
 - func_name: refine_center
   module_path: skxray.calibration

vttools/vtmods/utils.py

@@ -33,7 +33,7 @@
 # POSSIBILITY OF SUCH DAMAGE.                                          #
 ########################################################################
 from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+                        )
 import six
 from bubblegum.qt_widgets import query_widget
 from logging import Handler
@@ -44,6 +44,8 @@
 from .broker import search
 import numpy as np
 from metadataStore.utilities.utility import get_data_keys
+import enaml
+from enaml.qt.qt_application import QtApplication
 import logging
 logger = logging.getLogger(__name__)
 
@@ -153,6 +155,13 @@ def search_databroker(search_dict):
 #                                             unique_id_func=gen_unique_id)
 
 
+from bubblegum.xrf.model.xrf_model import XRF
+with enaml.imports():
+    from bubblegum.xrf.view.xrf_view import XrfGui
+
+xrf_view = XrfGui()
+xrf_view.xrf_model = XRF()
+
 def setup_bnl_menu():
     """
     Creates and hooks up a BNL specific menu in the main window
@@ -162,10 +171,14 @@ def setup_bnl_menu():
     menu_bar = bw.menuBar()
 
     bnl_menu = menu_bar.addMenu("BNL")
+    print('\n\n\n\n\n\nBNL Menu Added\n\n\n\n\n\n\n\n\n')
 
     def foo():
         print('menu bar clicked!')
         # query_window.show()
+        xrf_view.show()
+
+
     bnl_menu.addAction("demo", foo)
 
 

vttools/vtmods/vis.py

@@ -36,7 +36,7 @@
 Created on Apr 29, 2014
 '''
 from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+                        )
 import six
 from PyQt4 import QtCore, QtGui
 from vistrails.core.modules.vistrails_module import (Module, ModuleSettings,

vttools/wrap_lib.py

@@ -34,7 +34,7 @@
 ########################################################################
 
 from __future__ import (absolute_import, division,
-                        print_function, unicode_literals)
+                        print_function)
 import six
 import inspect
 import importlib
@@ -487,11 +487,11 @@ def define_input_ports(docstring, func):
             port_is_enum = is_enum
             port_enum_list = enum_list
             # start with the easy ones
-            pdict = {'name': port_name,
-                     'label': short_description,
+            pdict = {'name': str(port_name),
+                     'label': str(short_description),
                      'optional': is_optional,
-                     'signature': pytype_to_vtsig(param_type=port_type,
-                                                  param_name=port_name)}
+                     'signature': str(pytype_to_vtsig(param_type=port_type,
+                                                  param_name=port_name))}
 
             # deal with if the function as an enum attribute
             if hasattr(func, port_name):
@@ -518,8 +518,8 @@ def define_input_ports(docstring, func):
                 port_enum_list = f_enums
                 port_is_enum = True
             if port_is_enum:
-                pdict['entry_type'] = 'enum'
-                pdict['values'] = port_enum_list
+                pdict['entry_type'] = str('enum')
+                pdict['values'] = [str(x) for x in port_enum_list]
 
             logger.debug('port_param_dict: {0}'.format(pdict))
             input_ports.append(IPort(**pdict))
@@ -576,7 +576,7 @@ def define_output_ports(docstring):
                 if the_type == '':
                     continue
                 the_type = _check_alt_types(the_type)
-                output_ports.append(OPort(name=the_name,
+                output_ports.append(OPort(name=str(the_name),
                                           signature=pytype_to_vtsig(
                                               param_type=the_type,
                                               param_name=the_name)))