Changes in / [ce94504:dceff6e] in sasview


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  • .travis.yml

    r58918de ra4974fa  
    1212  system_site_packages: true 
    1313before_install: 
    14   - 'if [ $TRAVIS_PYTHON_VERSION == "2.7" ]; then sudo apt-get update;sudo apt-get install python-numpy python-scipy python-matplotlib libhdf5-serial-dev python-h5py fglrx opencl-headers python-pyopencl; fi' 
     14  - 'if [ $TRAVIS_PYTHON_VERSION == "2.7" ]; then sudo apt-get update;sudo apt-get install python-numpy python-scipy python-matplotlib; fi' 
    1515 
    1616install: 
    1717  - pip install -r build_tools/requirements.txt 
    18  
    19 before_script: 
    20   - "export DISPLAY=:99.0" 
    21   - "sh -e /etc/init.d/xvfb start" 
    22   - sleep 3 # give xvfb some time to start 
    23    
    2418script: 
    25   - export WORKSPACE=/home/travis/build/SasView/ 
    26   - cd $WORKSPACE 
    27   - git clone --depth=50 --branch=master https://github.com/SasView/sasmodels.git sasmodels 
     19  - export WORKSPACE=/home/travis/build/SasView/sasview/ 
    2820  - export PYTHONPATH=$WORKSPACE/sasview-install:$WORKSPACE/utils:$PYTHONPATH 
    29   - cd $WORKSPACE 
    30   - ls -ltr 
    3121  - if [ ! -d "utils" ]; then mkdir utils; fi 
    32   - /bin/sh -xe sasview/build_tools/travis_build.sh 
    33 #  - /bin/sh -xe sasview/build_tools/jenkins_linux_test.sh 
     22  - /bin/sh -xe build_tools/jenkins_linux_build.sh 
     23  - /bin/sh -xe build_tools/jenkins_linux_test.sh 
    3424  - export LC_ALL=en_US.UTF-8 
    3525  - export LANG=en_US.UTF-8 
    36 #  - python setup.py docs; echo 0 
    37 #  - python setup.py bdist_egg --skip-build 
     26  - python setup.py docs; echo 0 
     27  - python setup.py bdist_egg --skip-build 
    3828 

  • sasview/__init__.py

    r4ac4caa r86eb046  
    22__build__ = "GIT_COMMIT" 
    33try: 
    4     import logging 
    54    import subprocess 
    65    import os 
    7     import platform 
    86    FNULL = open(os.devnull, 'w') 
    9     if platform.system() == "Windows": 
    10         args = ['git', 'describe', '--tags'] 
    11     else: 
    12         args = ['git describe --tags'] 
    13     git_revision = subprocess.check_output(args, 
     7    git_revision = subprocess.check_output(['git', 'rev-parse', 'HEAD'], 
    148                    stderr=FNULL, 
    159                    shell=True) 
    1610    __build__ = str(git_revision).strip() 
    17 except subprocess.CalledProcessError as cpe: 
    18     logging.warning("Error while determining build number\n  Using command:\n %s \n Output:\n %s"% (cpe.cmd,cpe.output)) 
     11except: 
     12    import logging 
     13    import sys 
     14    logging.warning("Error while determining build number\n  %s" % sys.exc_value) 

  • src/sas/sascalc/dataloader/readers/cansas_reader.py

    r654e8e0 r5f26aa4  
    6262    type_name = "canSAS" 
    6363    invalid = True 
    64     frm = "" 
    6564    ## Log messages and errors 
    6665    logging = None 
    … …  
    139138                    for entry in entry_list: 
    140139                        # Create a new DataInfo object for every <SASentry> 
     140 
    141141 
    142142                        # Set the file name and then parse the entry. 
    … …  
    183183        return self.output 
    184184 
    185     def _parse_entry(self, dom, recurse=False): 
     185    def _parse_entry(self, dom): 
    186186        """ 
    187187        Parse a SASEntry - new recursive method for parsing the dom of 
    … …  
    192192        """ 
    193193 
    194         if not self._is_call_local() and not recurse: 
     194        frm = inspect.stack()[1] 
     195        if not self._is_call_local(frm): 
    195196            self.reset_state() 
    196197            self.add_data_set() 
    … …  
    200201        self.base_ns = "{0}{1}{2}".format("{", \ 
    201202                            CANSAS_NS.get(self.cansas_version).get("ns"), "}") 
     203        tagname = '' 
     204        tagname_original = '' 
    202205 
    203206        # Go through each child in the parent element 
    … …  
    222225                    self._initialize_new_data_set() 
    223226                ## Recursion step to access data within the group 
    224                 self._parse_entry(node, True) 
     227                self._parse_entry(node) 
    225228                if tagname == "SASsample": 
    226229                    self.current_datainfo.sample.name = name 
    … …  
    434437                length = len(self.names) - 1 
    435438            self.parent_class = self.names[length] 
    436         if not self._is_call_local() and not recurse: 
    437             self.frm = "" 
     439        if not self._is_call_local(frm): 
    438440            self.add_data_set() 
    439441            empty = None 
    … …  
    446448 
    447449 
    448     def _is_call_local(self): 
    449         """ 
    450  
    451         """ 
    452         if self.frm == "": 
    453             inter = inspect.stack() 
    454             self.frm = inter[2] 
    455         mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "") 
     450    def _is_call_local(self, frm=""): 
     451        """ 
     452 
     453        :return: 
     454        """ 
     455        if frm == "": 
     456            frm = inspect.stack()[1] 
     457        mod_name = frm[1].replace("\\", "/").replace(".pyc", "") 
    456458        mod_name = mod_name.replace(".py", "") 
    457459        mod = mod_name.split("sas/") 
    … …  
    834836        # If the calling function was not the cansas reader, return a minidom 
    835837        #      object rather than an lxml object. 
    836         self.frm = inspect.stack()[1] 
    837         doc, entry_node = self._check_origin(entry_node, doc) 
     838        frm = inspect.stack()[1] 
     839        doc, entry_node = self._check_origin(entry_node, doc, frm) 
    838840        return doc, entry_node 
    839841 
    … …  
    12301232                self.append(node, entry_node) 
    12311233 
    1232     def _check_origin(self, entry_node, doc): 
     1234    def _check_origin(self, entry_node, doc, frm): 
    12331235        """ 
    12341236        Return the document, and the SASentry node associated with 
    … …  
    12401242        :param doc: entire xml tree 
    12411243        """ 
    1242         if not self.frm: 
    1243             self.frm = inspect.stack()[1] 
    1244         mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "") 
     1244        if not frm: 
     1245            frm = inspect.stack()[1] 
     1246        mod_name = frm[1].replace("\\", "/").replace(".pyc", "") 
    12451247        mod_name = mod_name.replace(".py", "") 
    12461248        mod = mod_name.split("sas/") 

  • src/sas/sasgui/guiframe/media/graph_help.rst

    rf9b0c81 re68c9bf  
    4242plot window. 
    4343 
    44 .. note::  
    45     *If a residuals graph (when fitting data) is hidden, it will not show up 
    46     after computation.* 
     44*NOTE! If a residuals graph (when fitting data) is hidden, it will not show up 
     45after computation.* 
    4746 
    4847Dragging a plot 
    … …  
    6867After zooming in on a a region, the *left arrow* or *right arrow* buttons on 
    6968the toolbar will switch between recent views. 
    70  
    71 The axis range can also be specified manually.  To do so go to the *Graph Menu* 
    72 (see Invoking_the_graph_menu_ for further details), choose the *Set Graph Range* 
    73 option and enter the limits in the pop box. 
    7469 
    7570*NOTE! If a wheel mouse is available scrolling the wheel will zoom in/out 
    … …  
    121116^^^^^^^^^^^^^^^^^^^ 
    122117 
    123 It is possible to make custom modifications to plots including: 
     118From the *Graph Menu* (see Invoking_the_graph_menu_) it is also possible to 
     119make some custom modifications to plots, including: 
    124120 
    125121*  changing the plot window title 
    126 *  changing the default legend location and toggling it on/off 
    127 *  changing the axis label text 
    128 *  changing the axis label units 
    129 *  changing the axis label font & font colour 
     122*  changing the axis legend locations 
     123*  changing the axis legend label text 
     124*  changing the axis legend label units 
     125*  changing the axis legend label font & font colour 
    130126*  adding/removing a text string 
    131127*  adding a grid overlay 
    132  
    133 The legend and text strings can be drag and dropped around the plot 
    134  
    135 These options are accessed through the *Graph Menu* (see Invoking_the_graph_menu_) 
    136 and selecting *Modify Graph Appearance* (for axis labels, grid overlay and 
    137 legend position) or *Add Text* to add textual annotations, selecting font, color, 
    138 style and size. *Remove Text* will remove the last annotation added. To change 
    139 the legend. *Window Title* allows a custom title to be entered instead of Graph 
    140 x.  
    141128 
    142129Changing scales 
    … …  
    247234selected data will be removed from the plot. 
    248235 
    249 .. note:: 
    250     The Remove data set action cannot be undone. 
     236*NOTE! This action cannot be undone.* 
    251237 
    252238Show-Hide error bars 
    … …  
    262248In the *Dataset Menu* (see Invoking_the_dataset_menu_), select *Modify Plot 
    263249Property* to change the size, color, or shape of the displayed marker for the 
    264 chosen dataset, or to change the dataset label that appears in the plot legend 
    265 box. 
     250chosen dataset, or to change the dataset label that appears on the plot. 
    266251 
    267252.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    307292average. 
    308293 
    309 .. note:: 
    310     The displayed average only updates when input focus is moved back to 
    311     that window; ie, when the mouse pointer is moved onto that plot. 
     294*NOTE! The displayed average only updates when input focus is moved back to 
     295that window; ie, when the mouse pointer is moved onto that plot.* 
    312296 
    313297Selecting *Box Sum* automatically brings up the 'Slicer Parameters' dialog in 
    … …  
    375359.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    376360 
    377 .. note::  This help document was last modified by Paul Butler, 05 September, 2016 
     361.. note::  This help document was last changed by Steve King, 01May2015 

  • src/sas/sasgui/perspectives/fitting/pagestate.py

    r654e8e0 r7673ecd  
    15691569                    if output[ind].run_name is not None\ 
    15701570                        and len(output[ind].run_name) != 0: 
    1571                         if isinstance(output[ind].run_name, dict): 
    1572                             name = output[ind].run_name.keys()[0] 
    1573                         else: 
    1574                             name = output[ind].run_name 
     1571                        name = output[ind].run_name 
    15751572                    else: 
    15761573                        name = original_fname 

  • src/sas/sasgui/perspectives/invariant/invariant_panel.py

    r654e8e0 rcb93b40  
    830830        """ 
    831831        try: 
    832             if key in ['compute_num', 'file', 'is_time_machine', 'state_num']: 
    833                 return 
    834             else: 
    835                 attr = getattr(self, key) 
     832            attr = getattr(self, key) 
    836833            if attr.__class__.__name__ == "StaticText": 
    837834                return 
    838             if value in ["True", "False", True, False]: 
    839                 value = bool(value) 
    840             else: 
     835            if type(value) is not bool: 
    841836                value = str(value) 
    842837            attr.SetValue(value) 

  • src/sas/sasgui/perspectives/pr/media/pr_help.rst

    r0391dae rb64b87c  
    1515*P(r)* is set to be equal to an expansion of base functions of the type 
    1616 
    17 .. math:: 
    18   \Phi_{n(r)} = 2 r sin(\frac{\pi n r}{D_{max}}) 
     17  |bigphi|\_n(r) = 2.r.sin(|pi|\ .n.r/D_max) 
    1918 
    20 The coefficient of each base function in the expansion is found by performing 
     19The coefficient of each base function in the expansion is found by performing  
    2120a least square fit with the following fit function 
    2221 
    23 .. math:: 
     22  |chi|\ :sup:`2` = |bigsigma|\ :sub:`i` [ I\ :sub:`meas`\ (Q\ :sub:`i`\ ) - I\ :sub:`th`\ (Q\ :sub:`i`\ ) ] :sup:`2` / (Error) :sup:`2` + Reg_term 
    2423 
    25   \chi^2=\frac{\sum_i (I_{meas}(Q_i)-I_{th}(Q_i))^2}{error^2}+Reg\_term 
    26    
     24where I\ :sub:`meas`\ (Q) is the measured scattering intensity and  
     25I\ :sub:`th`\ (Q) is the prediction from the Fourier transform of the *P(r)*  
     26expansion.  
    2727 
    28 where $I_{meas}(Q_i)$ is the measured scattering intensity and $I_{th}(Q_i)$ is 
    29 the prediction from the Fourier transform of the *P(r)* expansion.  
    30  
    31 The $Reg\_term$ term is a regularization term set to the second derivative  
    32 $d^2P(r)/d^2r$ integrated over $r$. It is used to produce a smooth *P(r)* output. 
     28The *Reg_term* term is a regularization term set to the second derivative  
     29d\ :sup:`2`\ *P(r)* / dr\ :sup:`2` integrated over *r*. It is used to produce a  
     30smooth *P(r)* output. 
    3331 
    3432.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    4745   system. 
    4846 
    49 P(r) inversion requires that the background be perfectly subtracted.  This is 
    50 often difficult to do well and thus many data sets will include a background. 
    51 For those cases, the user should check the "estimate background" box and the 
    52 module will do its best to estimate it. 
    53  
    54 The P(r) module is constantly computing in the background what the optimum 
    55 *number of terms* should be as well as the optimum *regularization constant*. 
    56 These are constantly updated in the buttons next to the entry boxes on the GUI. 
    57 These are almost always close and unless the user has a good reason to choose 
    58 differently they should just click on the buttons to accept both.  {D_max} must 
    59 still be set by the user.  However, besides looking at the output, the user can 
    60 click the explore button which will bring up a graph of chi^2 vs Dmax over a 
    61 range around the current Dmax.  The user can change the range and the number of 
    62 points to explore in that range.  They can also choose to plot several other 
    63 parameters as a function of Dmax including: I0, Rg, Oscillation parameter, 
    64 background, positive fraction, and 1-sigma positive fraction. 
    65  
    6647.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    6748 
    … …  
    7455.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    7556 
    76 .. note::  This help document was last modified by Paul Butler, 05 September, 2016 
     57.. note::  This help document was last changed by Steve King, 01May2015 
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