Changeset 668c38b in sasmodels

Timestamp:

Apr 6, 2017 5:27:16 AM (7 years ago)

Author:

Adam Washington <adam.washington@…>

Branches:

master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

133103b

Parents:

9f91afe (diff), 650c6d2 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'master' into sesans_tof

Files:

• .travis.yml (modified) (1 diff)
• LICENSE.txt (modified) (1 diff)
• sasmodels/compare.py (modified) (13 diffs)
• sasmodels/core.py (modified) (1 diff)
• sasmodels/data.py (modified) (3 diffs)
• sasmodels/direct_model.py (modified) (1 diff)
• sasmodels/generate.py (modified) (1 diff)
• sasmodels/models/hayter_msa.py (modified) (1 diff)
• sasmodels/rst2html.py (modified) (2 diffs)
• sasmodels/sesans.py (modified) (3 diffs)

.travis.yml

@@ -1 @@
-# Test Travis CL
-
 language: python
 python:
-  - "2.7"
-# whitelist
+- '2.7'
 branches:
   only:
-    - master
-# command to install dependencies
+  - master
 virtualenv:
   system_site_packages: true
 before_install:
-  - sudo apt-get update;
-  - sudo apt-get install python-numpy python-scipy
-#  - sudo apt-get install opencl-headers
-
+- sudo apt-get update;
+- sudo apt-get install python-numpy python-scipy
 install:
-#  - pip install pyopencl
-  - pip install bumps
-  - pip install unittest-xml-reporting
+- pip install bumps
+- pip install unittest-xml-reporting
 script:
-  - export WORKSPACE=/home/travis/build/SasView/sasmodels/
-  - python -m sasmodels.model_test dll all
+- export WORKSPACE=/home/travis/build/SasView/sasmodels/
+- python -m sasmodels.model_test dll all
+notifications:
+  slack:
+    secure: xNAUeSu1/it/x9Q2CSg79aw1LLc7d6mLpcqSCTeKROp71RhkFf8VjJnJm/lEbKHNC8yj5H9UHrz5DmzwJzI+6oMt4NdEeS6WvGhwGY/wCt2IcJKxw0vj1DAU04qFMS041Khwclo6jIqm76DloinXvmvsS+K/nSyQkF7q4egSlwA=

LICENSE.txt

@@ -1 @@
-This program is in the public domain.
+Copyright (c) 2009-2017, SasView Developers
+All rights reserved.
 
-Individual files may be copyright different authors, with licences that
-allow modification and redistribution in source or binary form with or
-without modification, and a disclaimer of warranty.
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

sasmodels/compare.py

@@ -30 +30 @@
 
 import sys
+import os
 import math
 import datetime
@@ -40 +41 @@
 from . import kerneldll
 from . import exception
-from .data import plot_theory, empty_data1D, empty_data2D
+from .data import plot_theory, empty_data1D, empty_data2D, load_data
 from .direct_model import DirectModel
 from .convert import revert_name, revert_pars, constrain_new_to_old
@@ -85 +86 @@
     -html shows the model docs instead of running the model
     -title="note" adds note to the plot title, after the model name
+    -data="path" uses q, dq from the data file
 
 Any two calculation engines can be selected for comparison:
@@ -544 +546 @@
     'f32': '32',
     'f64': '64',
+    'float16': '16',
+    'float32': '32',
+    'float64': '64',
+    'float128': '128',
     'longdouble': '128',
 }
@@ -747 +753 @@
     comp = opts['engines'][1] if have_comp else None
     data = opts['data']
+    use_data = have_base ^ have_comp
 
     # Plot if requested
@@ -763 +770 @@
     if have_base:
         if have_comp: plt.subplot(131)
-        plot_theory(data, base_value, view=view, use_data=False, limits=limits)
+        plot_theory(data, base_value, view=view, use_data=use_data, limits=limits)
         plt.title("%s t=%.2f ms"%(base.engine, base_time))
         #cbar_title = "log I"
@@ -769 +776 @@
         if have_base: plt.subplot(132)
         if not opts['is2d'] and have_base:
-            plot_theory(data, base_value, view=view, use_data=False, limits=limits)
-        plot_theory(data, comp_value, view=view, use_data=False, limits=limits)
+            plot_theory(data, base_value, view=view, use_data=use_data, limits=limits)
+        plot_theory(data, comp_value, view=view, use_data=use_data, limits=limits)
         plt.title("%s t=%.2f ms"%(comp.engine, comp_time))
         #cbar_title = "log I"
@@ -784 +791 @@
             err[err>cutoff] = cutoff
         #err,errstr = base/comp,"ratio"
-        plot_theory(data, None, resid=err, view=errview, use_data=False)
+        plot_theory(data, None, resid=err, view=errview, use_data=use_data)
         if view == 'linear':
             plt.xscale('linear')
@@ -834 +841 @@
 VALUE_OPTIONS = [
     # Note: random is both a name option and a value option
-    'cutoff', 'random', 'nq', 'res', 'accuracy', 'title',
+    'cutoff', 'random', 'nq', 'res', 'accuracy', 'title', 'data',
     ]
 
@@ -951 +958 @@
         'html'      : False,
         'title'     : None,
+        'data'      : None,
     }
     engines = []
@@ -971 +979 @@
         elif arg.startswith('-cutoff='):   opts['cutoff'] = float(arg[8:])
         elif arg.startswith('-random='):   opts['seed'] = int(arg[8:])
-        elif arg.startswith('-title'):     opts['title'] = arg[7:]
+        elif arg.startswith('-title='):    opts['title'] = arg[7:]
+        elif arg.startswith('-data='):     opts['data'] = arg[6:]
         elif arg == '-random':  opts['seed'] = np.random.randint(1000000)
         elif arg == '-preset':  opts['seed'] = -1
@@ -1112 +1121 @@
 
     # Create the computational engines
-    data, _ = make_data(opts)
+    if opts['data'] is not None:
+        data = load_data(os.path.expanduser(opts['data']))
+    else:
+        data, _ = make_data(opts)
     if n1:
         base = make_engine(model_info, data, engines[0], opts['cutoff'])
@@ -1142 +1154 @@
     show html docs for the model
     """
-    import wx  # type: ignore
-    from .generate import view_html_from_info
-    app = wx.App() if wx.GetApp() is None else None
-    view_html_from_info(opts['def'][0])
-    if app: app.MainLoop()
-
+    import os
+    from .generate import make_html
+    from . import rst2html
+
+    info = opts['def'][0]
+    html = make_html(info)
+    path = os.path.dirname(info.filename)
+    url = "file://"+path.replace("\\","/")[2:]+"/"
+    rst2html.view_html_qtapp(html, url)
 
 def explore(opts):

sasmodels/core.py

@@ -250 +250 @@
         dtype = "longdouble"
     elif dtype == "half":
-        dtype = "f16"
+        dtype = "float16"
 
     # Convert dtype string to numpy dtype.

sasmodels/data.py

@@ -54 +54 @@
     if data is None:
         raise IOError("Data %r could not be loaded" % filename)
+    if hasattr(data, 'x'):
+        data.qmin, data.qmax = data.x.min(), data.x.max()
+        data.mask = (np.isnan(data.y) if data.y is not None
+                     else np.zeros_like(data.x, dtype='bool'))
     return data
 
@@ -348 +352 @@
     # data, but they already handle the masking and graph markup already, so
     # do not repeat.
-    if hasattr(data, 'lam'):
+    if hasattr(data, 'isSesans') and data.isSesans:
         _plot_result_sesans(data, None, None, use_data=True, limits=limits)
     elif hasattr(data, 'qx_data'):
@@ -376 +380 @@
     *Iq_calc* is the raw theory values without resolution smearing
     """
-    if hasattr(data, 'lam'):
+    if hasattr(data, 'isSesans') and data.isSesans:
         _plot_result_sesans(data, theory, resid, use_data=True, limits=limits)
     elif hasattr(data, 'qx_data'):

sasmodels/direct_model.py

@@ -192 +192 @@
 
         # interpret data
-        if hasattr(data, 'lam'):
+        if hasattr(data, 'isSesans') and data.isSesans:
             self.data_type = 'sesans'
         elif hasattr(data, 'qx_data'):

sasmodels/generate.py

@@ -928 +928 @@
     from . import rst2html
     url = "file://"+dirname(info.filename)+"/"
-    rst2html.wxview(make_html(info), url=url)
+    rst2html.view_html(make_html(info), url=url)
 
 def demo_time():

sasmodels/models/hayter_msa.py

@@ -74 +74 @@
     ["radius_effective", "Ang", 20.75,   [0, inf],    "volume", "effective radius of charged sphere"],
     ["volfraction",   "None",     0.0192, [0, 0.74],   "", "volume fraction of spheres"],
-    ["charge",        "e",   19.0,    [0, inf],    "", "charge on sphere (in electrons)"],
-    ["temperature",   "K",  318.16,   [0, inf],    "", "temperature, in Kelvin, for Debye length calculation"],
-    ["concentration_salt",      "M",    0.0,    [-inf, inf], "", "conc of salt, moles/litre, 1:1 electolyte, for Debye length"],
+    ["charge",        "e",   19.0,    [0, 200],    "", "charge on sphere (in electrons)"],
+    ["temperature",   "K",  318.16,   [0, 450],    "", "temperature, in Kelvin, for Debye length calculation"],
+    ["concentration_salt",      "M",    0.0,    [0, inf], "", "conc of salt, moles/litre, 1:1 electolyte, for Debye length"],
     ["dielectconst",  "None",    71.08,   [-inf, inf], "", "dielectric constant (relative permittivity) of solvent, default water, for Debye length"]
     ]

sasmodels/rst2html.py

@@ -29 +29 @@
 from docutils.writers.html4css1 import HTMLTranslator
 from docutils.nodes import SkipNode
-
-def wxview(html, url="", size=(850, 540)):
-    import wx
-    from wx.html2 import WebView
-    frame = wx.Frame(None, -1, size=size)
-    view = WebView.New(frame)
-    view.SetPage(html, url)
-    frame.Show()
-    return frame
-
-def view_rst(filename):
-    from os.path import expanduser
-    with open(expanduser(filename)) as fid:
-        rst = fid.read()
-    html = rst2html(rst)
-    wxview(html)
 
 def rst2html(rst, part="whole", math_output="mathjax"):
@@ -155 +139 @@
     assert replace_dollar(u"a (again $in parens$) a") == u"a (again :math:`in parens`) a"
 
-def view_rst_app(filename):
+def load_rst_as_html(filename):
+    from os.path import expanduser
+    with open(expanduser(filename)) as fid:
+        rst = fid.read()
+    html = rst2html(rst)
+    return html
+
+def wxview(html, url="", size=(850, 540)):
+    import wx
+    from wx.html2 import WebView
+    frame = wx.Frame(None, -1, size=size)
+    view = WebView.New(frame)
+    view.SetPage(html, url)
+    frame.Show()
+    return frame
+
+def qtview(html, url=""):
+    try:
+        from PyQt5.QtWebKitWidgets import QWebView
+        from PyQt5.QtCore import QUrl
+    except ImportError:
+        from PyQt4.QtWebkit import QWebView
+        from PyQt4.QtCore import QUrl
+    helpView = QWebView()
+    helpView.setHtml(html, QUrl(url))
+    helpView.show()
+    return helpView
+
+def view_html_wxapp(html, url=""):
     import wx  # type: ignore
     app = wx.App()
-    view_rst(filename)
+    frame = wxview(html, url)
     app.MainLoop()
 
+def view_html_qtapp(html, url=""):
+    import sys
+    try:
+        from PyQt5.QtWidgets import QApplication
+    except ImportError:
+        from PyQt4.QtGui import QApplication
+    app = QApplication([])
+    frame = qtview(html, url)
+    sys.exit(app.exec_())
+
+def view_rst_app(filename, qt=False):
+    import os
+    html = load_rst_as_html(filename)
+    url="file://"+os.path.abspath(filename)+"/"
+    if qt:
+        view_html_qtapp(html, url)
+    else:
+        view_html_wxapp(html, url)
 
 if __name__ == "__main__":
     import sys
-    view_rst_app(sys.argv[1])
+    view_rst_app(sys.argv[1], qt=True)
 

sasmodels/sesans.py

@@ -41 +41 @@
     _H0 = None # type: np.ndarray
 
-    def __init__(self, z, SElength, zaccept, Rmax):
+    def __init__(self, z, SElength, lam, zaccept, Rmax):
         # type: (np.ndarray, float, float) -> None
         #import logging; logging.info("creating SESANS transform")
         self.q = z
-        self._set_hankel(SElength, zaccept, Rmax)
+        self._set_hankel(SElength, lam, zaccept, Rmax)
 
     def apply(self, Iq):
@@ -54 +54 @@
         return P
 
-    def _set_hankel(self, SElength, zaccept, Rmax):
+    def _set_hankel(self, SElength, lam, zaccept, Rmax):
         # type: (np.ndarray, float, float) -> None
         # Force float32 arrays, otherwise run into memory problems on some machines
@@ -71 +71 @@
         H = np.float32(dq/(2*pi)) * j0(repSE*repq) * repq
 
+        replam = np.tile(lam, (q.size, 1))
+        reptheta = np.arcsin(repq*replam/2*np.pi)
+        mask = reptheta > zaccept
+        H[mask] = 0
+
         self.q_calc = q
         self._H, self._H0 = H, H0