updated xray examples and changed path.exists with isfile since this was what I meant

mcutils.py

@@ -518,7 +518,7 @@ def downloadPDB(pdbID,outFileName=None):
   if (outFileName is None):
     outFileName = pdbID+".pdb"
   folder = os.path.dirname(outFileName)
-  if (folder != '' and not os.path.exists(folder)):
+  if (folder != '' and not os.path.isdir(folder)):
     os.makedirs(folder)
   f=open(outFileName,"w")
   f.write( "".join(lines) )
@@ -1301,9 +1301,8 @@ def fac(n):
 
 
 def define_colors(fname="colorbrewer_all_schemes.json"):
-  if not os.path.exists(fname):
+  if not os.path.isfile(fname):
     fname = os.path.dirname(os.path.realpath(__file__)) + "/" + fname
-  if not os.path.exists(fname):
     print("Cannot find colorbrewer_all_schemes.json can't continue")
     print(fname)
     return

storage.py

@@ -167,7 +167,7 @@ class DataStorage(dict):
     if isinstance(fileOrDict,dict):
       d = fileOrDict
     elif isinstance(fileOrDict,str):
-      if os.path.exists(fileOrDict):
+      if os.path.isfile(fileOrDict):
         d = read(fileOrDict)
       else:
         self.filename=fileOrDict

xray/azav.py

@@ -107,7 +107,7 @@ def getAI(poni,folder=None):
     ai = pyFAI.azimuthalIntegrator.AzimuthalIntegrator(**poni)
   elif isinstance(poni,str):
     # look is file exists in cwd
-    if os.path.exists(poni):
+    if os.path.isfilee(poni):
       ai = pyFAI.load(poni)
     # if file does not exist look for one with that name around
     else:
@@ -123,7 +123,7 @@ def getAI(poni,folder=None):
       # look for file
       for path in folders:
         fname = path + "/" + poni
-        if os.path.exists(fname):
+        if os.path.isfile(fname):
           log.info("Found poni file %s",fname)
           break
         else:
@@ -197,7 +197,7 @@ def doFolder(folder,files='*.edf*',nQ = 1500,force=False,mask=None,
  """
   if storageFile == 'auto': storageFile = folder + "/" + "pyfai_1d.h5"
 
-  if os.path.exists(storageFile) and not force:
+  if os.path.isfile(storageFile) and not force:
     saved = storage.DataStorage(storageFile)
   else:
     saved = None

xray/example_main_salen.py

@@ -55,18 +55,15 @@ def prepareLog():
 prepareLog()
 
 def defineCalibrants(dmin=3):
-  from pyFAI import calibrant
-  c120 = calibrant.Cell(a=10.297,b=10.716,c=13.955,alpha=72.22,beta=70.45,gamma=74.13)
-  p120 = np.pi*2/ np.asarray( list(c120.d_spacing(dmin=dmin).keys()) ).astype(float)
-  p120.sort()
-  c300 = calibrant.Cell(a=10.485,b=11.015,c=14.280,alpha=74.61,beta=69.29,gamma=75.29)
-  p300 = np.pi*2/ np.asarray( list(c300.d_spacing(dmin=dmin).keys()) ).astype(float)
-  p300.sort()
-  return xray.storage.DataStorage( dict(p120=p120, c120=c120,p300=p300,c300=c300) )
+  c120 = xray.cell.Triclinic(a=10.297,b=10.716,c=13.955,alpha=72.22,beta=70.45,gamma=74.13)
+  p120,_ = c120.reflection_list()
+  c300 = xray.cell.Triclinic(a=10.485,b=11.015,c=14.280,alpha=74.61,beta=69.29,gamma=75.29)
+  p300,_ = c300.reflection_list()
+  return xray.storage.DataStorage( p120=p120, c120=c120,p300=p300,c300=c300) 
 
 def readCalculations(folder="../fesalen/cif",force=False,plot=False):
   npz = folder + "/fesalen_calc.npz"
-  if not os.path.exists(npz) or force:
+  if not os.path.isfile(npz) or force:
     ret = dict()
     for T in ("120LS","200HS","300HS"):
       # calculated with lambda = 1 Ang
@@ -104,41 +101,37 @@ def findCenter(cen=(484,479.5),dist=0.251):
 def removeBaseline(folder,qlims=(0.5,2.5),max_iter=30,force=False):
   if isinstance(folder,int): folder = g_default_folder%folder
   fname    = folder + "/pyfai_1d_nobaseline"+id9.default_extension
-  if not os.path.exists(fname) or force:
-    data = azav(folder,doRemoveBaseline=False)
+  if not os.path.isfile(fname) or force:
+    log.info("Calling azav with default parameters")
+    data = azav(folder,withBaseline=False)
     # first peak (around 0.6) is weak and requires special care ...
-    data.q,data.data = xray.utils.removeBackground(data.q,data.data,xlims=qlims,
-                max_iter=max_iter,background_regions=[ (0,0.58) ])
+    data.q,data.data = xray.utils.removeBackground(data.q,data.data,
+      xlims=qlims,max_iter=max_iter,background_regions=[ (0,0.58) ])
     data.save(fname)
   else:
     data = xray.storage.read(fname)
   return data
 
 def azav(folder,nQ=3000,force=False,saveChi=True,mask=g_default_mask,
-         doRemoveBaseline=True):
-  if isinstance(folder,int): folder = g_default_folder%folder
-  if isinstance(mask,int):
-    files = xray.utils.getFiles(folder,"*.edf*")
-    img   = xray.azav.pyFAIread(files[0])
-    temp = np.ones_like(img,dtype=bool)
-    temp[:mask] = False
-    mask = temp
-  azav = id9.doFolder_azav(folder,nQ=nQ,force=force,mask=mask,saveChi=saveChi)
-  if doRemoveBaseline: removeBaseline(folder)
-  return azav
+         withBaseline=True):
+  if withBaseline:
+    data=removeBaseline(folder)
+  else:
+    data = id9.doFolder_azav(folder,nQ=nQ,force=force,mask=mask,
+      saveChi=saveChi)
+  return data
 
 def datared(folder,monitor=(0.5,4),showPlot=True,errMask=5,chi2Mask=2,
             qlims=(0.5,3),withBaseline=False,forceDatared=False,
             select=slice(None),**kw):
   if isinstance(folder,int): folder = g_default_folder%folder
-  def_ext = id9.default_extension
+  data = azav(folder,withBaseline=withBaseline)
   extension = def_ext if withBaseline else "_nobaseline" + def_ext
   # storage files to use
   diffFile = folder + "/diffs" + extension
-  azavFile = folder + "/pyfai_1d" + extension
 
-  if not os.path.exists(diffFile) or forceDatared:
-    data,diffs = id9.doFolder_dataRed(azavFile,monitor=monitor,
+  if not os.path.isfile(diffFile) or forceDatared:
+    data,diffs = id9.doFolder_dataRed(data,monitor=monitor,
                  errMask=errMask,chi2Mask=chi2Mask,qlims=qlims,
                  outStorageFile=diffFile)
   else:

xray/example_main_tiox.py

@@ -17,18 +17,12 @@ def readCalc():
   calc = dict()
   for name,fname in zip(names,fnames):
     q,i=np.loadtxt(fold + "%s.xye.q"%fname,unpack=True)
-    calc[name] = xray.storage.DataStorage( dict( q=q, i=i ) )
+    calc[name] = dict( q=q, i=i ) 
   return xray.storage.DataStorage(calc)
 
 calc = readCalc()
 
-def azav(folder,nQ=1500,force=False,saveChi=True,mask=470):
-  if isinstance(mask,int):
-    files = xray.utils.getFiles(folder,"*.edf*")
-    img   = xray.azav.read(files[0])
-    temp = np.ones_like(img,dtype=bool)
-    temp[:mask] = False
-    mask = temp
+def azav(folder,nQ=1500,force=False,saveChi=True,mask='y>470'):
   return id9.doFolder_azav(folder,nQ=nQ,force=force,mask=mask,saveChi=saveChi)
 
 def datared(folder,monitor=(1,5),showPlot=True,**kw):

xray/id9.py

@@ -52,7 +52,7 @@ def doFolder_dataRed(azavStorage,monitor=None,funcForAveraging=np.nanmean,
   if isinstance(azavStorage,storage.DataStorage):
     data = azavStorage
     folder = os.path.dirname(data.filename) if data.filename is not None else "./"
-  elif os.path.exists(azavStorage):
+  elif os.path.isfile(azavStorage):
     folder = os.path.dirname(azavStorage)
     data = storage.DataStorage(azavStorage)
   else:

xray/utils.py

@@ -184,7 +184,7 @@ def saveTxt(fname,q,data,headerv=None,info=None,overwrite=True,columns=''):
         info = dictionary (saved as '# key : value') or string
         headerv = vector to be used as header or string
   """
-  if os.path.exists(fname) and not overwrite:
+  if os.path.isfile(fname) and not overwrite:
     log.warn("File %s exists, returning",fname)
     return
   if isinstance(info,dict):