Merge pull request #43 from newville/master

update python XDI module for latest version

Author: newville

python/lib/__init__.py

@@ -2,22 +2,22 @@
    Xas Data Interchange Format
 
    Matthew Newville <[email protected]>
-   last update:  2011-Dec-01 
-      
+   last update:  2015-Mar-24
+
 == License:
    To the extent possible, the authors have waived all rights
    granted by copyright law and related laws for the code and
    documentation that make up the XAS Data Library.  While
    information about Authorship may be retained in some files
    for historical reasons, this work is hereby placed in the
    Public Domain.  This work is published from: United States.
-   
+
 == Overview:
    The xdi module provides a way to read/write files in the
    XAS Data Interchange format
-   
+
 """
-__version__ = '0.2.0'
+__version__ = '0.2.1'
 
 from . import xdi
 XDIFile = xdi.XDIFile

python/lib/xdi.py

@@ -6,13 +6,9 @@
 import ctypes
 import ctypes.util
 
-__version__ = '1.1.0'
+__version__ = '1.2.0'
 
-try:
-    from numpy import array, exp, log, sin, arcsin
-    HAS_NUMPY = True
-except ImportError:
-    HAS_NUMPY = False
+from numpy import array, exp, log, sin, arcsin
 
 PI = 3.14159265358979323846
 RAD2DEG  = 180.0/PI
@@ -38,8 +34,9 @@ class XDIFileStruct(ctypes.Structure):
                 ('edge',          ctypes.c_char_p),
                 ('comments',      ctypes.c_char_p),
                 ('error_line',    ctypes.c_char_p),
+                ('error_message', ctypes.c_char_p),
                 ('array_labels',  ctypes.c_void_p),
-                ('outer_label',   ctypes.c_char_p),                
+                ('outer_label',   ctypes.c_char_p),
                 ('array_units',   ctypes.c_void_p),
                 ('meta_families', ctypes.c_void_p),
                 ('meta_keywords', ctypes.c_void_p),
@@ -62,7 +59,6 @@ def get_xdilib():
     """make initial connection to XDI dll"""
     global XDILIB
     if XDILIB is None:
-        add_dot2path()
         dllpath  = ctypes.util.find_library('xdifile')
         load_dll = ctypes.cdll.LoadLibrary
         if os.name == 'nt':
@@ -71,6 +67,7 @@ def get_xdilib():
         XDILIB.XDI_errorstring.restype   = ctypes.c_char_p
     return XDILIB
 
+
 class XDIFileException(Exception):
     """XDI File Exception: General Errors"""
     def __init__(self, msg, **kws):
@@ -107,29 +104,36 @@ def __init__(self, filename=None):
 
     def write(self, filename):
         "write out an XDI File"
-        print 'Writing XDI file not currently supported'
+        print( 'Writing XDI file not currently supported')
 
     def read(self, filename=None):
         """read validate and parse an XDI datafile into python structures
         """
         if filename is None and self.filename is not None:
             filename = self.filename
-
         pxdi = ctypes.pointer(XDIFileStruct())
         self.status = out = self.xdilib.XDI_readfile(filename, pxdi)
         if out < 0:
-            msg = self.xdilib.XDI_errorstring(out)
+            msg =  self.xdilib.XDI_errorstring(out)
+            self.xdilib.XDI_cleanup(pxdi, out)
             msg = 'Error reading XDIFile %s\n%s' % (filename, msg)
             raise XDIFileException(msg)
 
         xdi = pxdi.contents
         for attr in dict(xdi._fields_):
             setattr(self, attr, getattr(xdi, attr))
-
         pchar = ctypes.c_char_p
         self.array_labels = (self.narrays*pchar).from_address(xdi.array_labels)[:]
-        self.array_units  = (self.narrays*pchar).from_address(xdi.array_units)[:]
-        
+        arr_units  = (self.narrays*pchar).from_address(xdi.array_units)[:]
+        self.array_units = []
+        self.array_addrs = []
+        for unit in arr_units:
+            addr = ''
+            if '||' in unit:
+                unit, addr = [x.strip() for x in unit.split('||', 1)]
+            self.array_units.append(unit)
+            self.array_addrs.append(addr)
+
         mfams = (self.nmetadata*pchar).from_address(xdi.meta_families)[:]
         mkeys = (self.nmetadata*pchar).from_address(xdi.meta_keywords)[:]
         mvals = (self.nmetadata*pchar).from_address(xdi.meta_values)[:]
@@ -143,7 +147,7 @@ def read(self, filename=None):
 
         parrays = (xdi.narrays*ctypes.c_void_p).from_address(xdi.array)[:]
         rawdata = [(xdi.npts*ctypes.c_double).from_address(p)[:] for p in parrays]
-        
+
         nout = xdi.nouter
         outer, breaks = [], []
         if nout > 1:
@@ -153,17 +157,16 @@ def read(self, filename=None):
             delattr(self, attr)
         self.outer_array    = array(outer)
         self.outer_breakpts = array(breaks)
-        
-        
-        if HAS_NUMPY:
-            rawdata = array(rawdata)
-            rawdata.shape = (self.narrays, self.npts)
+
+
+        rawdata = array(rawdata)
+        rawdata.shape = (self.narrays, self.npts)
         self.rawdata = rawdata
         self._assign_arrays()
-
         for attr in ('nmetadata', 'narray_labels', 'meta_families',
                      'meta_keywords', 'meta_values', 'array'):
             delattr(self, attr)
+        self.xdilib.XDI_cleanup(pxdi, 0)
 
     def _assign_arrays(self):
         """assign data arrays for principle data attributes:
@@ -173,14 +176,10 @@ def _assign_arrays(self):
         xunits = 'eV'
         xname = None
         ix = -1
-        if HAS_NUMPY:
-            self.rawdata = array(self.rawdata)
+        self.rawdata = array(self.rawdata)
 
         for idx, name in enumerate(self.array_labels):
-            if HAS_NUMPY:
-                dat = self.rawdata[idx,:]
-            else:
-                dat = [d[idx] for d in self.rawdata]
+            dat = self.rawdata[idx,:]
             setattr(self, name, dat)
             if name in ('energy', 'angle'):
                 ix = idx
@@ -189,12 +188,15 @@ def _assign_arrays(self):
                 if units is not None:
                     xunits = units
 
-        if not HAS_NUMPY:
-            return
-
         # convert energy to angle, or vice versa
-        if ix >= 0 and 'd_spacing' in self.attrs['mono']:
-            dspace = float(self.attrs['mono']['d_spacing'])
+        monodat = {}
+        if 'mono' in  self.attrs:
+            monodat = self.attrs['mono']
+        elif 'monochromator' in  self.attrs:
+            monodat = self.attrs['monochromator']
+
+        if ix >= 0 and 'd_spacing' in monodat:
+            dspace = float(monodat['d_spacing'])
             if dspace < 0: dspace = 0.001
             omega = PLANCK_HC/(2*dspace)
             if xname == 'energy' and not hasattr(self, 'angle'):

python/tests/test1.py

@@ -3,39 +3,23 @@
 sys.path.insert(0, '../')
 import lib as  xdi
 
-testfile = os.path.join('..', '..', 'perl', 't', 'xdi.aps10id')
+testfile = os.path.join('..', '..', 'data', 'cu_metal_10k.xdi')
 if len(sys.argv) > 1:
     testfile = sys.argv[1]
-    
-f = xdi.XDIFile(testfile)
-
-print( 'Read file ', f.fname, ' Version: ', f.file_version)
-# print( '==Pre-Defined Fields==')
-# for key in sorted(xdi.DEFINED_FIELDS):
-#     attr = key.lower().replace('-','_')
-#     if hasattr(f, attr):
-#         print( '  %s: %s' % (key, getattr(f, attr)))
-# 
-# print( '==Extra Fields')
-# for key, val in f.attributes.items():
-#     print( '  %s: %s' % (key, val))
-
-print( '==User Comments:')
-print( '\n'.join(f.comments))
-print( '==Labels:')
-print( f.labels, f.has_numpy)
 
-if f.has_numpy:
-    print( '==Data: numeric array', f.data.shape)
-
-else:
-    print( '==Data: lists', len(f.data))
-
-for key in sorted(f.columns):
-    out = None
-    if f.column_data[key] is not None:
-        print key, f.columns[key], len(f.column_data[key]), f.column_data[key][:3]
+f = xdi.XDIFile(testfile)
 
+print( 'Read file ', f.filename)
 
+#print( '==Extra Fields')
+#for key in dir(f):
+#    if not key.startswith('_'):
+#        print( '  %s: %s' % (key, getattr(f, key)))
 
-f.write('out3.xdi')
+print( '==File:', f.filename)
+print( '==Element, Edge: ', f.element, f.edge)
+print( '==Extra Version:', f.extra_version)
+print( '==User Comments:', f.comments)
+print( '==Array Labels:', f.array_labels)
+print( '==Array Npts:', f.npts)
+print( '==Data: array shape, type:', f.rawdata.shape, f.rawdata.dtype)