From d17b9caa7fbfee84c55f64a8d948007a7e0cf926 Mon Sep 17 00:00:00 2001
From: Marco Cammarata <marco.cammarata@univ-rennes1.fr>
Date: Thu, 9 Mar 2017 23:20:57 +0100
Subject: [PATCH] added id9 log file parser

---
 xray/__init__.py |  1 +
 xray/id9.py      | 43 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 44 insertions(+)

diff --git a/xray/__init__.py b/xray/__init__.py
index 5ae30d7..e57bba7 100644
--- a/xray/__init__.py
+++ b/xray/__init__.py
@@ -4,6 +4,7 @@ from . import mask
 from . import peaks
 from . import cell
 from . import filters
+from . import id9
 try:
   from . import azav
 except ImportError:
diff --git a/xray/id9.py b/xray/id9.py
index 1561045..7c90bef 100644
--- a/xray/id9.py
+++ b/xray/id9.py
@@ -48,6 +48,49 @@ def readDelayFromDiagnostic(fname):
   delays = np.round(delays.astype(float),12)
   return collections.OrderedDict( zip(files,delays) )
 
+def _findDark(line):
+  _,value = line.split(":")
+  return float(value)
+
+def _delayToNum(delay):
+  if delay.decode('ascii') == 'off':
+    delay = -10
+  else:
+    delay=utils.strToTime(delay)
+  return delay
+
+def findLogFile(folder):
+  files = utils.getFiles(folder,basename='*.log')
+  files.remove(os.path.join(folder,"diagnostics.log"))
+  logfile = files[0]
+  if len(files)>1: log.warn("Found more than one *.log file that is not diagnostics.log: %s"%files)
+  return logfile
+
+def readLogFile(fnameOrFolder,subtractDark=False):
+  """ read id9 style logfile """
+  if os.path.isdir(fnameOrFolder):
+    fname = findLogFile(fnameOrFolder)
+  else:
+    fname = fnameOrFolder
+  f = open(fname,"r")
+  lines = f.readlines()
+  f.close()
+  lines = [line.strip() for line in lines]
+  darks = {}
+  for line in lines:
+    if line.find("pd1 dark/sec")>=0: darks['pd1ic'] = _findDark(line)
+    if line.find("pd2 dark/sec")>=0: darks['pd2ic'] = _findDark(line)
+    if line.find("pd3 dark/sec")>=0: darks['pd3ic'] = _findDark(line)
+    if line.find("pd4 dark/sec")>=0: darks['pd4ic'] = _findDark(line)
+  for iline,line in enumerate(lines):
+    if line.lstrip()[0] != "#": break
+  data=np.genfromtxt(fname,skip_header=iline-1,names=True,comments="%",dtype=None,converters = {'delay': lambda s: _delayToNum(s)})
+  if subtractDark:
+    for diode in ['pd1ic','pd2ic','pd3ic','pd4ic']:
+      if diode in darks: data[diode]=data[diode]-darks[diode]*data['timeic']
+  return data
+
+
 
 def doFolder_azav(folder,nQ=1500,files='*.edf*',force=False,mask=None,
   saveChi=True,poni='pyfai.poni',storageFile='auto',dark=9.9,zingerFilter=30,qlims=(0,10),