Merge branch 'master' into py37-sasgui

.gitignore

@@ -38,6 +38,7 @@ Thumbs.db
 /docs/sphinx-docs/node-package.json
 
 # test outputs
+/.eggs
 /test/pr_inversion/test/test_output.txt
 /test/sasdataloader/test/plugins.zip
 /test/sasdataloader/test/test_log.txt

LICENSE.TXT

@@ -1,4 +1,4 @@
-Copyright (c) 2009-2018, SasView Developers
+Copyright (c) 2009-2019, SasView Developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

conftest.py

@@ -0,0 +1,7 @@
+"""
+Pytest configuration file.
+"""
+
+# Prepare the runtime environment for the tests
+import run
+run.prepare()

docs/sphinx-docs/source/conf.py

@@ -25,6 +25,12 @@
 print("-- path --")
 print("\n".join(sys.path))
 
+#need to import src.sas.sasview init to access version number and dates
+#use abspath as above to locate then import
+sasview_path = os.path.abspath('../../../src/sas')
+sys.path.append(sasview_path)
+import sas.sasview
+
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -70,17 +76,18 @@
 master_doc = 'index'
 
 # General information about the project.
+copyright_date = sas.sasview.__release_date__
 project = u'SasView'
-copyright = u'2018, The SasView Project'
+copyright = u'%s, The SasView Project' % copyright_date
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '4.2'
-# The full version, including alpha/beta/rc tags.
-release = '4.2.0'
+version = ".".join(sas.sasview.__version__.split(".", 2)[0:2]) 
+# The full version, including ax/bx tags Note strict version is enforced.
+release = sas.sasview.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/sphinx-docs/source/user/RELEASE.rst

@@ -9,6 +9,36 @@ Release Notes
 Features
 ========
 
+New in Version 4.2.1
+--------------------
+The major changes for this point release were to fix several problems with using
+the built in editor to create new models and to bring the NXcanSAS reader into
+compliance with the final published specification.  The orignal reader was
+based on a draft version of the specification.  As an early adopter,
+interpretation and implementation of the spec was iterated with all producers
+of NXcanSAS reduced data known to the SasView team in order to ensure
+compatibility and verify the implementation.  A few other enhancements and bug
+fixed were also introduced such as cleaning up the resolution section of the
+fitting page GUI, increasing the max size range allowed in the corfunc
+analysis, and adding the incomplete gamma function to the python library. 
+
+Resolved Issues
+^^^^^^^^^^^^^^^
+* Fixes #  976:	CanSas HDF reader will not read all valid CanSas HDF (NXcanSAS) files
+* Fixes # 1074:	Add incomplete gamma function to sasmodels
+* Fixes # 1111:	Convert all input Q units to 1/A
+* Fixes # 1129:	NXcanSAS writer not writing all meta data
+* Fixes # 1142:	Plugin framework is broken
+* Fixes # 1183:	Test from creating new model reset all parameters to default in all open FitPages
+* Fixes # 1188:   Colons removed from magnetic parameter names to address Python variable issue - done in 4.2. but documented in 4.2.1
+* Fixes # 1205:	4.2 set weighting choice seems to be ignored.
+* Fixes # 1206:	Incorrect (and confusing) presentation of dQ from data in instrumental smearing section
+* Fixes # 1212:	Bug in Iqxqy plotting non rectangular / square matrices?
+* Fixes # 1221:	ABS reader does not read in USANS data properly	GitHub
+* Fixes # 1222:	smearing options incorrect on show2D and show1D in fitpage14: Loading a saved project is really really slow
+* Fixes # 1223:	Expand permitted range of transformed data in Corfunc implementation
+
+
 New in Version 4.2.0
 --------------------
 This release heralds many improvements and a host of bug fixes, along with
@@ -125,7 +155,7 @@ Bug Fixes
 * Fixes # 776: angular dispersity
 * Fixes # 784: Add 3D integral to Correlation Function analysis
 * Fixes # 786: core_shell_parallelepiped 1-D model is incorrect
-* Fixes # 818: “report button” followed by “save” makes an empty pdf file???
+* Fixes # 818: “report button” followed by “save” makes an empty pdf file???
 * Fixes # 830: Check compliance of loader against NXcanSAS-1.0 release
 * Fixes # 838: Fix model download from marketplace
 * Fixes # 848: can't save analysis when only one fit page

installers/license.txt

@@ -19,7 +19,7 @@ may read here: https://github.com/SasView/sasview/blob/master/LICENSE.TXT
 
 SasView is free to download and use, including for commercial purposes.
 
-� 2009-2018 UMD, UTK, NIST, ORNL, ISIS, ESS, ANSTO, ILL, TUD, DLS, BAM  
+� 2009-2019 UMD, UTK, NIST, ORNL, ISIS, ESS, ANSTO, ILL, TUD, DLS, BAM  
 
 
 If you use SasView to do productive scientific research that leads to 

setup.py

@@ -55,25 +55,6 @@
 CURRENT_SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
 SASVIEW_BUILD = os.path.join(CURRENT_SCRIPT_DIR, "build")
 
-# TODO: build step should not be messing with existing installation!!
-sas_dir = os.path.join(os.path.expanduser("~"), '.sasview')
-if os.path.isdir(sas_dir):
-    f_path = os.path.join(sas_dir, "sasview.log")
-    if os.path.isfile(f_path):
-        os.remove(f_path)
-    f_path = os.path.join(sas_dir, "categories.json")
-    if os.path.isfile(f_path):
-        os.remove(f_path)
-    f_path = os.path.join(sas_dir, 'config', "custom_config.py")
-    if os.path.isfile(f_path):
-        os.remove(f_path)
-    #f_path = os.path.join(sas_dir, 'plugin_models')
-    # if os.path.isdir(f_path):
-    #     for f in os.listdir(f_path):
-    #         if f in plugin_model_list:
-    #             file_path =  os.path.join(f_path, f)
-    #             os.remove(file_path)
-
 
 # Optionally clean before build.
 dont_clean = 'update' in sys.argv

src/sas/_config.py

@@ -85,6 +85,7 @@ def make_custom_config_path(user_dir):
 
 def setup_custom_config(app_dir, user_dir):
     path = make_custom_config_path(user_dir)
+    #logger.info("custom config path %s", path)
     if not os.path.isfile(path):
         try:
             # if the custom config file does not exist, copy the default from
@@ -93,18 +94,19 @@ def setup_custom_config(app_dir, user_dir):
         except Exception:
             logger.error("Could not copy default custom config.")
 
+    custom_config = load_custom_config(path)
+
     #Adding SAS_OPENCL if it doesn't exist in the config file
     # - to support backcompability
-    if not "SAS_OPENCL" in open(path).read():
+    if not hasattr(custom_config, "SAS_OPENCL"):
+        custom_config.SAS_OPENCL = None
         try:
-            open(config_file, "a+").write("SAS_OPENCL = \"None\"\n")
+            open(path, "a+").write("SAS_OPENCL = \"None\"\n")
         except Exception:
             logger.error("Could not update custom config with SAS_OPENCL.")
 
-    custom_config = load_custom_config(path)
     return custom_config
 
-
 def load_custom_config(path):
     if os.path.exists(path):
         try:
@@ -116,4 +118,4 @@ def load_custom_config(path):
 
     from sas.sasview import custom_config
     logger.info("GuiManager custom_config defaults to sas.sasview.custom_config")
-    return custom_config
+    return custom_config

src/sas/sascalc/calculator/instrument.py

@@ -127,7 +127,11 @@ def set_size(self, size=[]):
         if len(size) == 0:
             self.size = 0
         else:
-            self.size = size
+            # TODO: Make sure detector size is number of pixels
+            # Could be detector dimensions in e.g., mm, but
+            # the resolution calculator assumes it is pixels.
+            # Being pixels, it has to be integers rather than float
+            self.size = [int(s) for s in size]
             validate(size[0])
 
     def set_pix_size(self, size=[]):

src/sas/sascalc/calculator/resolution_calculator.py

@@ -1006,8 +1006,8 @@ def _get_detector_qxqy_pixels(self):
         detector_offset = 0
         try:
             detector_offset = self.sample2detector_distance[1]
-        except:
-            logger.error(sys.exc_value)
+        except Exception as exc:
+            logger.error(exc)
 
         # detector size in [no of pix_x,no of pix_y]
         detector_pix_nums_x = self.detector_size[0]
@@ -1093,8 +1093,8 @@ def _get_detector_qxqy_pixels(self):
             output.data = inten
             output.qx_data = qx_value
             output.qy_data = qy_value
-        except:
-            logger.error(sys.exc_value)
+        except Exception as exc:
+            logger.error(exc)
 
         return output
 

src/sas/sascalc/corfunc/corfunc_calculator.py

@@ -29,21 +29,20 @@ def __init__(self, f, g, start, stop):
             self.g = g
             self.start = start
             self.stop = stop
-            self._lastx = []
-            self._lasty = []
+            self._lastx = np.empty(0, dtype='d')
+            self._lasty = None
 
         def __call__(self, x):
             # If input is a single number, evaluate the function at that number
             # and return a single number
-            if type(x) == float or type(x) == int:
+            if isinstance(x, (float, int)):
                 return self._smoothed_function(np.array([x]))[0]
             # If input is a list, and is different to the last input, evaluate
             # the function at each point. If the input is the same as last time
             # the function was called, return the result that was calculated
             # last time instead of explicity evaluating the function again.
-            elif self._lastx == [] or x.tolist() != self._lastx.tolist():
-                self._lasty = self._smoothed_function(x)
-                self._lastx = x
+            if not np.array_equal(x, self._lastx):
+                self._lastx, self._lasty = x, self._smoothed_function(x)
             return self._lasty
 
         def _smoothed_function(self,x):
@@ -87,7 +86,7 @@ def set_data(self, data, scale=1):
             return
         # Only process data of the class Data1D
         if not issubclass(data.__class__, Data1D):
-            raise ValueError("Data must be of the type DataLoader.Data1D")
+            raise ValueError("Correlation function cannot be computed with 2D data.")
 
         # Prepare the data
         new_data = Data1D(x=data.x, y=data.y)
@@ -245,7 +244,9 @@ def _porod(self, q, K, sigma, bg):
     def _fit_guinier(self, q, iq):
         """Fit the Guinier region of the curve"""
         A = np.vstack([q**2, np.ones(q.shape)]).T
-        return lstsq(A, np.log(iq))
+        # CRUFT: numpy>=1.14.0 allows rcond=None for the following default
+        rcond = np.finfo(float).eps * max(A.shape)
+        return lstsq(A, np.log(iq), rcond=rcond)
 
     def _fit_porod(self, q, iq):
         """Fit the Porod region of the curve"""

src/sas/sascalc/corfunc/transform_thread.py

@@ -44,7 +44,7 @@ def compute(self):
             # ----- 3D Correlation Function -----
             # gamma3(R) = 1/R int_{0}^{R} gamma1(x) dx
             # trapz uses the trapezium rule to calculate the integral
-            mask = xs <= 200.0 # Only calculate gamma3 up to x=200 (as this is all that's plotted)
+            mask = xs <= 1000.0 # Only calculate gamma3 up to x=1000 (as this is all that's plotted)
             # gamma3 = [trapz(gamma1[:n], xs[:n])/xs[n-1] for n in range(2, len(xs[mask]) + 1)]j
             # gamma3.insert(0, 1.0) # Gamma_3(0) is defined as 1
             n = len(xs[mask])
@@ -78,7 +78,7 @@ def compute(self):
         self.update(msg="Fourier transform completed.")
 
         transform1 = Data1D(xs, gamma1)
-        transform3 = Data1D(xs[xs <= 200], gamma3)
+        transform3 = Data1D(xs[xs <= 1000], gamma3)
         idf = Data1D(xs, idf)
 
         transforms = (transform1, transform3, idf)

src/sas/sascalc/data_util/calcthread.py

@@ -5,30 +5,25 @@
 #
 from __future__ import print_function
 
-import traceback
 import sys
 import logging
+import traceback
+from time import sleep
+
 try:
     import _thread as thread
 except ImportError: # CRUFT: python 2 support
     import thread
-
-if sys.platform.count("darwin") > 0:
-    import time
-    stime = time.time()
-
-    def clock():
-        return time.time() - stime
-
-    def sleep(t):
-        return time.sleep(t)
-else:
-    from time import clock
-    from time import sleep
+try:
+    from time import perf_counter as clock
+except ImportError: # CRUFT: python < 3.3
+    if sys.platform.count("darwin") > 0:
+        from time import time as clock
+    else:
+        from time import clock
 
 logger = logging.getLogger(__name__)
 
-
 class CalcThread:
     """Threaded calculation class.  Inherit from here and specialize
     the compute() method to perform the appropriate operations for the
@@ -247,7 +242,7 @@ def exception(self):
             try:
                 self.exception_handler(*sys.exc_info())
                 return
-            except Exception:
+            except Exception as exc:
                 pass
         logger.error(traceback.format_exc())
         #print 'CalcThread exception',

src/sas/sascalc/data_util/nxsunit.py

@@ -98,11 +98,10 @@ def _caret_optional(s):
     """
     Strip '^' from unit names.
 
-    * WARNING * this will incorrect transform 10^3 to 103.
+    * WARNING * this will incorrectly transform 10^3 to 103.
     """
-    s.update((k.replace('^',''),v)
-             for k, v in list(s.items())
-             if '^' in k)
+    stripped = [(k.replace('^',''),v) for k, v in s.items() if '^' in k]
+    s.update(stripped)
 
 def _build_all_units():
     distance = _build_metric_units('meter','m')
@@ -135,8 +134,9 @@ def _build_all_units():
 
     sld = { '10^-6 Angstrom^-2': 1e-6, 'Angstrom^-2': 1 }
     Q = { 'invA': 1, 'invAng': 1, 'invAngstroms': 1, '1/A': 1,
+          '1/Angstrom': 1, '1/angstrom': 1, 'A^{-1}': 1, 'cm^{-1}': 1e-8,
           '10^-3 Angstrom^-1': 1e-3, '1/cm': 1e-8, '1/m': 1e-10,
-          'nm^-1': 0.1, '1/nm': 0.1, 'n_m^-1': 0.1 }
+          'nm^{-1}': 1, 'nm^-1': 0.1, '1/nm': 0.1, 'n_m^-1': 0.1 }
 
     _caret_optional(sld)
     _caret_optional(Q)
@@ -156,7 +156,7 @@ class Converter(object):
     # Note: a.u. stands for arbitrary units, which should return the default
     # units for that particular dimension.
     # Note: don't have support for dimensionless units.
-    unknown = {None:1, '???':1, '': 1, 'a.u.': 1}
+    unknown = {None:1, '???':1, '': 1, 'a.u.': 1, 'Counts': 1, 'counts': 1}
 
     def __init__(self, name):
         self.base = name

src/sas/sascalc/data_util/ordereddicttest.py

@@ -146,10 +146,10 @@ def test_copying(self):
                     OrderedDict(od),
                     ]):
             self.assert_(dup is not od)
-            self.assertEquals(dup, od)
-            self.assertEquals(list(dup.items()), list(od.items()))
-            self.assertEquals(len(dup), len(od))
-            self.assertEquals(type(dup), type(od))
+            self.assertEqual(dup, od)
+            self.assertEqual(list(dup.items()), list(od.items()))
+            self.assertEqual(len(dup), len(od))
+            self.assertEqual(type(dup), type(od))
 
     def test_repr(self):
         od = OrderedDict([('c', 1), ('b', 2), ('a', 3), ('d', 4), ('e', 5), ('f', 6)])

src/sas/sascalc/data_util/registry.py

@@ -147,4 +147,4 @@ def load(self, path, format=None):
         if last_exc is not None and len(loaders) != 0:
             # If file has associated loader(s) and they;ve failed
             raise last_exc
-        raise NoKnownLoaderException(e.message)  # raise generic exception
+        raise NoKnownLoaderException(str(message))  # raise generic exception

src/sas/sascalc/data_util/uncertainty.py

@@ -18,7 +18,7 @@
 
 import numpy as np
 
-from .import err1d
+from . import err1d
 from .formatnum import format_uncertainty
 
 __all__ = ['Uncertainty']