LLNL-PyDV 3.4.3__tar.gz

llnl_pydv-3.4.3/LICENSE

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+Copyright (c) 2011-2024, Lawrence Livermore National Security, LLC.
+Produced at the Lawrence Livermore National Laboratory  
+Written by Mason Kwiat, Douglas S. Miller, and Kevin Griffin, Ephraim Rusu, Sarah El-Jurf, Jorge Moreno
+e-mail: eljurf11@llnl.gov, moreno45@llnl.gov
+LLNL-CODE-507071
+All rights reserved.  
+  
+This file is part of PDV.  For details, see <https://lc.llnl.gov/confluence/pages/viewpage.action?spaceKey=PYDV&title=PyDV%3A+Python+Data+Visualizer>. 
+Please also read "Additional BSD Notice".
+    
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+      
+Redistributions of source code must retain the above copyright
+notice, this list of conditions and the disclaimer below.
+Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the disclaimer (as noted below)
+in the documentation and/or other materials provided with the
+distribution.  Neither the name of the LLNS/LLNL 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 LAWRENCE
+LIVERMORE NATIONAL SECURITY, LLC, THE U.S. DEPARTMENT OF ENERGY 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.
+           
+Additional BSD Notice  
+             
+1. This notice is required to be provided under our contract with
+the U.S.  Department of Energy (DOE).  This work was produced at
+Lawrence Livermore National Laboratory under Contract
+No. DE-AC52-07NA27344 with the DOE.
+               
+2. Neither the United States Government nor Lawrence Livermore
+National Security, LLC nor any of their employees, makes any
+warranty, express or implied, or assumes any liability or
+responsibility for the accuracy, completeness, or usefulness of any
+information, apparatus, product, or process disclosed, or represents
+that its use would not infringe privately-owned rights.
+                 
+3.  Also, reference herein to any specific commercial products,
+process, or services by trade name, trademark, manufacturer or
+otherwise does not necessarily constitute or imply its endorsement,
+recommendation, or favoring by the United States Government or
+Lawrence Livermore National Security, LLC.  The views and opinions
+of authors expressed herein do not necessarily state or reflect
+those of the United States Government or Lawrence Livermore National
+Security, LLC, and shall not be used for advertising or product
+endorsement purposes.

llnl_pydv-3.4.3/PKG-INFO

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+Metadata-Version: 2.1
+Name: LLNL-PyDV
+Version: 3.4.3
+Summary: PyDV: Python Data Visualizer
+Home-page: https://github.com/LLNL/PyDV
+License: BSD
+Author: Sarah El-Jurf
+Author-email: eljurf1@llnl.gov
+Maintainer: Sarah El-Jurf
+Maintainer-email: eljurf1@llnl.gov
+Requires-Python: >=3.6
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: End Users/Desktop
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: License :: Other/Proprietary License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Requires-Dist: PyQt5
+Requires-Dist: PySide2
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Project-URL: Bug Tracker, https://github.com/LLNL/PyDV/issues
+Project-URL: Documentation, https://pydv.readthedocs.io/en/latest/
+Project-URL: Discussions, https://github.com/LLNL/PyDV/discussions
+Description-Content-Type: text/markdown
+
+## PyDV 
+
+A 1D graphics and data analysis tool, heavily based on the ULTRA plotting tool.
+
+### PyDV Importable Interface Module ###
+You can now call most of PyDV's functionality from within a Python script. Below is an example of how to do this.
+        
+        import sys
+        sys.path.append("/usr/gapps/pydv/current")
+        import pydvpy as pydvif
+
+        curves = list()
+        curves.append(pydvif.span(1,10,6))
+        pydvif.save('myFile.txt', curves)
+        
+## Documentation
+
+[PyDV Users Manual](https://pydv.readthedocs.io/en/latest/) [![Documentation Status](https://readthedocs.org/projects/pydv/badge/?version=latest)](https://pydv.readthedocs.io/en/latest/?badge=latest)
+
+## License
+
+PyDV is distributed under the terms of the [BSD-3 License](LICENSE)
+
+All new contributions must be made under the [BSD-3 License](LICENSE)
+
+See [LICENSE](LICENSE) for details.
+
+LLNL-CODE-507071
+

llnl_pydv-3.4.3/README.md

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+## PyDV 
+
+A 1D graphics and data analysis tool, heavily based on the ULTRA plotting tool.
+
+### PyDV Importable Interface Module ###
+You can now call most of PyDV's functionality from within a Python script. Below is an example of how to do this.
+        
+        import sys
+        sys.path.append("/usr/gapps/pydv/current")
+        import pydvpy as pydvif
+
+        curves = list()
+        curves.append(pydvif.span(1,10,6))
+        pydvif.save('myFile.txt', curves)
+        
+## Documentation
+
+[PyDV Users Manual](https://pydv.readthedocs.io/en/latest/) [![Documentation Status](https://readthedocs.org/projects/pydv/badge/?version=latest)](https://pydv.readthedocs.io/en/latest/?badge=latest)
+
+## License
+
+PyDV is distributed under the terms of the [BSD-3 License](LICENSE)
+
+All new contributions must be made under the [BSD-3 License](LICENSE)
+
+See [LICENSE](LICENSE) for details.
+
+LLNL-CODE-507071

llnl_pydv-3.4.3/pydv/NOTES

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+TO UPDATE TO LATEST VERSION, DO:
+
+hg pull https://dougmillerLLNL@bitbucket.org/dougmillerLLNL/pdv
+
+THEN
+
+chmod ugo+r *
+
+2015/05
+   Added 'savecsv' command.
+   
+2015/04
+   Added 'newcurve' command.
+   
+2013/04/12
+   Redefined norm so it does not divide by the interval.  This
+   definition is more  consistent with usual mathematical 
+   definitions of norm. Also, fixed bug in integrate() where if 
+   either xmin or xmax were zero, then the user supplied interval 
+   was ignored.
+
+2012/11/30
+   Added ability to change width of label column, upgraded regex
+   syntax documentation.
+
+2012/11/12
+   Made linespoints show up as o-o in the legend rather than -o-.
+
+2012/09/04
+   Added 'linespoints' mode for curves.  Syntax like the 'scatter'
+   mode command.
+
+2012/05/10
+   Ticks pretty much good, Owen added headerless reads.  Clear that 
+   we need a re-factoring of the code, several missed opportunities 
+   for encapsulation exist.
+
+2011/12/2
+   Working on ticks.  Currently does not run script xx correctly.
+
+2011/11/22
+   Added ability to read column formatted data, via '-gnu' command
+line argument or '.gnu' file suffix.
+
+2011/11/17
+   /usr/gapps/pdv/bin/pdv version wasn't the latest, updated that.
+
+2011/11/1
+   Set up on GoogleCode.  Went to Mercurial repo on code.google.com.
+   Also have bug tracker working on GoogleCode.
+
+2011/10/22
+   Making branches/dev branch, because tick work is messing up trunk.
+
+2011/10/11
+   Adding tick mark specification.
+

llnl_pydv-3.4.3/pydv/README.md

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+# README #
+
+## PDV is a 1D graphics and data analysis tool, heavily based on the ULTRA plotting tool. ##
+
+To use it, download the source, and run with Python.  You need pyside or pyqt4, matplotlib and numpy installed.
+
+### PyDV Importable Interface Module ###
+You can now call most of PyDV's functionality from within a Python script. Below is an example of how to do this.
+        
+        import sys
+        sys.path.append("/usr/gapps/pydv/2.0")
+        import pydvpy as pydvif
+
+        curves = list()
+        curves.append(pydvif.span(1,10,6))
+        pydvif.save('myFile.txt', curves)
+
+### Links ###
+* PDV Home Page: https://lc.llnl.gov/confluence/display/PYDV/PDV%3A+Python+Data+Visualizer 
+* PDV JIRA: https://lc.llnl.gov/jira/projects/PYDV
+* PDV Build and Test Results: https://lc.llnl.gov/bamboo/browse/PYDV-BUIL
+* Ultra User's Manual: https://wci.llnl.gov/codes/pact/ultra.html
+
+### Who do I talk to? ###
+
+* Sarah El-Jurf <eljurf1@llnl.gov>
+* Jorge Moreno <moreno45@llnl.gov>

llnl_pydv-3.4.3/pydv/__init__.py

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+__all__ = ["curve", "pdv", "pdvutil", "pdvnavbar", "pdvplot", "pydvpy"]

llnl_pydv-3.4.3/pydv/curve.py

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+# Copyright (c) 2011-2024, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory
+# Written by Mason Kwiat, Douglas S. Miller, and Kevin Griffin, Ephraim Rusu
+# e-mail: rusu1@llnl.gov
+# LLNL-CODE-507071
+# All rights reserved.
+
+# This file is part of PDV.  For details, see <URL describing code and
+# how to download source>. Please also read "Additional BSD Notice".
+
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+
+# Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the disclaimer below.
+# Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the disclaimer (as noted below)
+# in the documentation and/or other materials provided with the
+# distribution.  Neither the name of the LLNS/LLNL 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 LAWRENCE
+# LIVERMORE NATIONAL SECURITY, LLC, THE U.S. DEPARTMENT OF ENERGY 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.
+
+# Additional BSD Notice
+
+# 1. This notice is required to be provided under our contract with
+# the U.S.  Department of Energy (DOE).  This work was produced at
+# Lawrence Livermore National Laboratory under Contract
+# No. DE-AC52-07NA27344 with the DOE.
+
+# 2. Neither the United States Government nor Lawrence Livermore
+# National Security, LLC nor any of their employees, makes any
+# warranty, express or implied, or assumes any liability or
+# responsibility for the accuracy, completeness, or usefulness of any
+# information, apparatus, product, or process disclosed, or represents
+# that its use would not infringe privately-owned rights.
+
+# 3.  Also, reference herein to any specific commercial products,
+# process, or services by trade name, trademark, manufacturer or
+# otherwise does not necessarily constitute or imply its endorsement,
+# recommendation, or favoring by the United States Government or
+# Lawrence Livermore National Security, LLC.  The views and opinions
+# of authors expressed herein do not necessarily state or reflect
+# those of the United States Government or Lawrence Livermore National
+# Security, LLC, and shall not be used for advertising or product
+# endorsement purposes.
+
+import sys
+import numpy as np
+from scipy import interpolate, integrate
+
+
+class Curve(object):
+
+    name = ''
+    filename = ''
+    record_id = ''
+    xlabel = ''
+    ylabel = ''
+    title = ''
+    plotname = ''
+    color = ''
+    edited = False
+    scatter = False
+    linespoints = False
+    linewidth = None
+    linestyle = '-'
+    drawstyle = 'default'
+    dashes = None
+    hidden = False
+    x = np.empty(0)
+    y = np.empty(0)
+    ebar = None  # errorbar
+    erange = None  # errorrange
+    marker = '.'  # Use matplotlib markers when setting directly
+    markerstyle = None
+    markersize = 3
+    markerfacecolor = None
+    markeredgecolor = None
+    plotprecedence = 0
+    legend_show = True
+
+    def __init__(self, filename='', name='', record_id='', xlabel='', ylabel='', title='',
+                 step=False, xticks_labels=None):
+        self.filename = filename
+        self.name = name
+        self.record_id = record_id
+        self.xlabel = xlabel
+        self.ylabel = ylabel
+        self.title = title
+        self.step = step
+        self.xticks_labels = xticks_labels
+
+    def __add__(a, b):
+        c = Curve('', '')
+        c.drawstyle = a.drawstyle
+        c.plotname = str(a.plotname + ' + ' + b.plotname + ' ').strip('  ')
+        ia, ib = getinterp(a, b)
+        if ia.x is not None and ib.x is not None:
+            c.x = ia.x
+            c.y = ia.y + ib.y
+        return c
+
+    def __sub__(a, b):
+        c = Curve('', '')
+        c.drawstyle = a.drawstyle
+        c.plotname = str(a.plotname + ' - ' + b.plotname + ' ').strip('  ')
+        ia, ib = getinterp(a, b)
+        if ia.x is not None and ib.x is not None:
+            c.x = ia.x
+            c.y = ia.y - ib.y
+        return c
+
+    def __mul__(a, b):
+        c = Curve('', '')
+        c.drawstyle = a.drawstyle
+        c.plotname = str(a.plotname + ' * ' + b.plotname + ' ').strip('  ')
+        ia, ib = getinterp(a, b)
+        if ia.x is not None and ib.x is not None:
+            c.x = ia.x
+            c.y = ia.y * ib.y
+        return c
+
+    def __div__(a, b):
+        c = Curve('', '')
+        c.drawstyle = a.drawstyle
+        c.plotname = str(a.plotname + ' / ' + b.plotname + ' ').strip('  ')
+        ia, ib = getinterp(a, b)
+        if ia.x is not None and ib.x is not None:
+            c.x = ia.x
+
+            zero_indices = np.where(ib.y == 0)
+            for idx in zero_indices:
+                ib.y[idx] = 0.000000001
+
+            c.y = ia.y / ib.y
+            for idx in zero_indices:
+                c.y[idx] = float(sys.maxsize)
+
+        return c
+
+    def __truediv__(a, b):
+        c = Curve('', '')
+        c.drawstyle = a.drawstyle
+        c.plotname = str(a.plotname + ' / ' + b.plotname + ' ').strip('  ')
+        ia, ib = getinterp(a, b)
+        if ia.x is not None and ib.x is not None:
+            c.x = ia.x
+
+            zero_indices = np.where(ib.y == 0)
+            for idx in zero_indices:
+                ib.y[idx] = 0.000000001
+
+            c.y = ia.y / ib.y
+            for idx in zero_indices:
+                c.y[idx] = float(sys.maxsize)
+
+        return c
+
+    def __pow__(a, b):
+        c = Curve('', '')
+        c.drawstyle = a.drawstyle
+        c.plotname = str(a.plotname + '^' + str(b)).strip('  ')
+        c.x = np.array(a.x)
+        c.y = np.power(a.y, b)
+        nans = np.isnan(c.y)  # remove NaNs
+        c.x = c.x[~nans]
+        c.y = c.y[~nans]
+        return c
+
+    def __neg__(a):
+        c = Curve('', '')
+        c.drawstyle = a.drawstyle
+        c.plotname = str('-' + a.plotname)
+        c.x = np.array(a.x)
+        c.y = np.array(-a.y)
+        return c
+
+    def copy(self):
+        """
+        Return a new copy of the curve object
+        """
+
+        c = Curve(self.filename, self.name, self.record_id, self.xlabel, self.ylabel, self.title)
+        c.plotname = self.plotname
+        c.x = np.array(self.x)
+        c.y = np.array(self.y)
+        c.color = self.color
+        c.edited = self.edited
+        c.scatter = self.scatter
+        c.linespoints = self.linespoints
+        c.linewidth = self.linewidth
+        c.linestyle = self.linestyle
+        c.drawstyle = self.drawstyle
+        c.dashes = self.dashes
+        c.hidden = self.hidden
+        c.marker = self.marker
+        c.markerstyle = self.markerstyle
+        c.markersize = self.markersize
+        c.markeredgecolor = self.markeredgecolor
+        c.markerfacecolor = self.markerfacecolor
+        c.ebar = self.ebar
+        c.erange = self.erange
+        c.plotprecedence = self.plotprecedence
+
+        return c
+
+    def normalize(self):
+        """
+        Return a new normalized copy of the curve object
+        """
+
+        c = self.copy()
+
+        area0 = integrate.simpson(c.y, c.x)
+        c.y /= float(area0)
+        c.name = "Normalized %s" % self.plotname
+        return c
+
+
+def getinterp(a, b, left=None, right=None, samples=100, match='domain'):
+    """
+    Gets the interpolated and domain matched versions of the two curves.
+
+    :param a: Curve A
+    :type a: curve
+    :param b: Curve B
+    :type b: curve
+    :param left: Value to return for `x < a.x[0]`, default is `a.y[0]`.
+    :type left: float, optional
+    :param right: Value to return for `x > a.x[-1]`, default is `a.y[-1]`.
+    :type: right: float, optional
+    :param match {'domain','step'},optional: A string indicating how to interpolate the two curves
+    :type match: str
+    :returns: curve pair -- the interpolated and domain matched versions of a and b
+    """
+    if match == 'domain':
+        ux = list(set(a.x).union(set(b.x)))  # get union of xvals
+        ux.sort()
+
+        ia = a.copy()
+        ia.x = np.array(ux)
+        ia.y = np.interp(ux, a.x, a.y, left, right)  # interpolate y vals
+
+        ib = Curve('', '')
+        ib.x = np.array(ux)
+        ib.y = np.interp(ux, b.x, b.y, left, right)  # interpolate y vals
+
+        return ia, ib
+    elif match == 'step':
+        ax, step = np.linspace(min(a.x), max(a.x), num=samples, retstep=True)
+
+        bxsamples = int((max(b.x) - min(b.x)) / step)
+        if bxsamples < 1:
+            bxsamples = 1
+
+        bx = np.linspace(min(b.x), max(b.x), bxsamples)
+
+        ia = a.copy()
+        ia.x = ax
+        ia.y = np.interp(ax, a.x, a.y, left, right)  # interpolate y vals
+
+        ib = Curve('', '')
+        ib.x = bx
+        ib.y = np.interp(bx, b.x, b.y, left, right)  # interpolate y vals
+
+        return ia, ib
+    else:
+        raise ValueError("{} is not a supported option for match".format(match))
+
+
+def interp1d(a, num=100, retstep=False):
+    """
+    Gets the interpolated values of the curve with the specified number of samples.
+
+    :param a: Curve A
+    :type a: curve
+    :param num: Number of samples to generate. Default is 100. Must be non-negative.
+    :type: num: int, optional
+    :param retstep: return the spacing between samples
+    :type: retstep: bool, optional
+    :returns: ia: curve -- the interpolated and dimensions matched version of a
+              step: float, optional -- only returned if retstep is True. Size of the spacing between samples
+    """
+    num = int(num)
+    f = interpolate.interp1d(a.x, a.y, kind='linear', bounds_error=False, fill_value=0)
+
+    ia = a.copy()
+
+    if retstep:
+        ia.x, step = np.linspace(min(a.x), max(a.x), num=num, retstep=True)
+        ia.y = f(ia.x)
+        return ia, step
+    else:
+        ia.x = np.linspace(min(a.x), max(a.x), num=num, retstep=False)
+        ia.y = f(ia.x)
+        return ia
+
+
+def append(a, b):
+    """
+    Merge curve a and curve b over the union of their domains. Where domains overlap, take
+    the average of the curve's y-values.
+
+    :param a: Curve A
+    :type a: curve
+    :param b: Curve B
+    :type b: curve
+    :return: a new curve resulting from the merging of curve a and curve b
+    """
+    ux = list(set(a.x).union(set(b.x)))  # get union of xvals
+    ux.sort()
+
+    aub = Curve('', '')
+    aub.x = np.array(ux)
+    aub.y = np.zeros(len(aub.x))
+
+    for i in range(len(aub.x)):
+        xval = aub.x[i]
+
+        aidx = np.where(a.x == xval)[0]
+        bidx = np.where(b.x == xval)[0]
+
+        has_a = len(aidx) != 0
+        has_b = len(bidx) != 0
+
+        sum = float(0)
+        tot = 0
+
+        if has_a:
+            for idx in aidx:
+                sum += float(a.y[idx])
+                tot += 1
+
+        if has_b:
+            for idx in bidx:
+                sum += float(b.y[idx])
+                tot += 1
+
+        aub.y[i] = sum / float(tot)
+
+    return aub

llnl_pydv-3.4.3/pydv/pdv

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+#!/usr/bin/env /usr/apps/weave/weave-develop-cpu/bin/python3
+
+import sys
+import os
+
+sys.path.insert(0, os.path.dirname(__file__))
+
+# HPC Import
+try:
+    import pdv
+    pdv.Command().main()
+
+# Package Import
+except ImportError:
+    import pydv.pdv
+    pydv.pdv.Command().main()
+