Merge pull request #16 from NSLS-II-CHX/enh_chxtools_pkg

ENH: chxtools package update for 2.0.x
NSLS-II-CHX · Dec 20, 2017 · 0261082 · 0261082
2 parents eaef81d + 91dc6ba
commit 0261082
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diff --git a/chxtools/Time_Correlation_Functions.py b/chxtools/Time_Correlation_Functions.py
@@ -9,7 +9,7 @@
 import numpy as np
 import sys
 import time
-import skxray.core.roi as roi
+import skbeam.core.roi as roi
 from matplotlib import gridspec
 
 import itertools

diff --git a/chxtools/chx_wrapper.py b/chxtools/chx_wrapper.py
@@ -3,7 +3,8 @@
 by LW 03/20/2015
 some wrapper functions for ophyd
 """
-import Tkinter, tkFileDialog
+from __future__ import print_function
+
 
 def det_select(det):
     """
@@ -16,19 +17,19 @@ def det_select(det):
     calling sequence: det_select(det)
     """
     try:
-	rm_det=ascan.user_detectors[0].name
-	ascan.user_detectors.remove(session_mgr[rm_det])
+        rm_det=ascan.user_detectors[0].name
+        ascan.user_detectors.remove(session_mgr[rm_det])
         ascan.default_triggers = []
         ascan.default_detectors = []
-	print 'removed previous default detector: ',rm_det
-    except: print 'list of detectors appeared to be empty...'
-
+        print('removed previous default detector: {}'.format(rm_det))
+    except:
+        print('list of detectors appeared to be empty...')
+
     ascan.user_detectors.append(det)        # add detector
-    new_def_det=ascan.user_detectors[0].name    
-
-    print ''
-    print 'new default detector: ',new_def_det
-
+    new_def_det=ascan.user_detectors[0].name
+
+    print('\nnew default detector: {}'.format(new_def_det))
+
 
 def cw_ascan(mot,xmin,xmax,npoints,acqt='default',pos_ret=True):
     """
@@ -43,30 +44,32 @@ def cw_ascan(mot,xmin,xmax,npoints,acqt='default',pos_ret=True):
     WILL NOT WORK FOR A LIST OF DETECTORS!
     """
     # gather beamline information prior to starting the scan:
-    ini_motpos=caget(mot.record+'.RBV')
+    ini_motpos = caget(mot.record+'.RBV')
     # current detector:
-    acq_pv=session_mgr[ascan.user_detectors[0].name].pvname
-    
+    acq_pv = session_mgr[ascan.user_detectors[0].name].pvname
+
     # set different exposure time for the scan, if requested:
-    if acqt!='default':
+    if acqt != 'default':
         try:
-            ini_expt=caget(acq_pv[2]) # initial exposure time
+            ini_expt = caget(acq_pv[2]) # initial exposure time
             session_mgr[ascan.user_detectors[0].name].acquire_time = acqt
-            print 'successfully set exposure time to [s]: ',acqt 
-        except: print 'could not set exposure time to ',acqt
-
+            print('successfully set exposure time to [s]: {}'.format(acqt))
+        except:
+            print('could not set exposure time to {}'.format(acqt))
+
     # execute the scan
     ascan(mot,xmin,xmax,npoints)
-    
+
     # put beamline back into initial state
-    if pos_ret==True:
+    if pos_ret is True:
         caput(mot.record+'.VAL',ini_motpos)
-        print 'returned axes to: ',ini_motpos
-    if acqt!='default':
+        print('returned axes to: {}'.format(ini_motpos))
+    if acqt != 'default':
         try:
             session_mgr[ascan.user_detectors[0].name].acquire_time = ini_expt
-            print 'successfully reset exposure time to [s]: ',ini_expt 
-        except: print 'could not reset exposure time to ',ini_expt
+            print('successfully reset exposure time to [s]: {}'.format(ini_expt))
+        except:
+            print('could not reset exposure time to {}'.format(ini_expt))
 
 def cw_dscan(mot,mdx,pdx,npoints,acqt='default',pos_ret=True):
     """
@@ -78,25 +81,27 @@ def cw_dscan(mot,mdx,pdx,npoints,acqt='default',pos_ret=True):
     WILL NOT WORK FOR A LIST OF DETECTORS!
     """
     # current detector:
-    acq_pv=session_mgr[ascan.user_detectors[0].name].pvname
-    
+    acq_pv = session_mgr[ascan.user_detectors[0].name].pvname
+
     # set different exposure time for the scan, if requested:
-    if acqt!='default':
+    if acqt != 'default':
         try:
             ini_expt=caget(acq_pv[2]) # initial exposure time
             session_mgr[ascan.user_detectors[0].name].acquire_time = acqt
-            print 'successfully set exposure time to [s]: ',acqt 
-        except: print 'could not set exposure time to ',acqt
-
+            print('successfully set exposure time to [s]: {}'.format(acqt))
+        except:
+            print('could not set exposure time to {}'.format(acqt))
+
     # execute the scan
     dscan(mot,mdx,pdx,npoints)
-    #print 'finished scan'    
-    
-    if acqt!='default':
+    #print('finished scan')
+
+    if acqt != 'default':
         try:
             session_mgr[ascan.user_detectors[0].name].acquire_time = ini_expt
-            print 'successfully reset exposure time to [s]: ',ini_expt 
-        except: print 'could not reset exposure time to ',ini_expt
+            print('successfully reset exposure time to [s]: {}'.format(ini_expt))
+        except:
+            print('could not reset exposure time to {}'.format(ini_expt))
 
 def cw_CCDseries(folder,filename,detector,imnum='default',startn=1,acqt='default',acqperiod='default'):
     """
@@ -118,7 +123,7 @@ def cw_CCDseries(folder,filename,detector,imnum='default',startn=1,acqt='default
     # get the detector name::
     detector.pvname.split('}')[0]+'}'
     #get folder interactively:
-    
+
     if folder == 'ia':
       root=Tkinter.Tk()
       root.withdraw()
@@ -127,116 +132,125 @@ def cw_CCDseries(folder,filename,detector,imnum='default',startn=1,acqt='default
     # check whether target directory exists and create it, if it doesn't
     if not os.path.exists(folder):
       os.mkdir(folder)
-      os.chmod(folder,436) 	#make sure everybody can read an write
+      os.chmod(folder,436)      #make sure everybody can read an write
       os.chmod(folder,stat.S_IRWXO)
-      print 'successfully created new directory: ',folder
-
-
+      print('successfully created new directory: {}'.format(folder))
+
     # put folder:
     r=caput(detector.pvname.split('}')[0]+'}TIFF1:FilePath', folder)      # have some problem with syntax here...
-    if r==1:
-      print 'changed saving directory to: ',folder
-    else: print 'error: could not change directory for saving data files.'
+    if r == 1:
+        print('changed saving directory to: {}'.format(folder))
+    else:
+        print('error: could not change directory for saving data files.')
     # put the filename:
     r=caput(detector.pvname.split('}')[0]+'}TIFF1:FileName', filename)      # have some problem with syntax here...
-    if r==1:
-      print 'filename for saving: ',filename
-    else: print 'error: could not change file name for saving.'
+    if r == 1:
+        print('filename for saving: {}'.format(filename))
+    else:
+        print('error: could not change file name for saving.')
 
-
     # put start number
     caput(detector.pvname.split('}')[0]+'}TIFF1:FileNumber',startn)
-    
+
     #gather information about current camera settings
-    acq_pv=session_mgr[ascan.user_detectors[0].name].pvname
-    ini_acq=caget(acq_pv.split('}')[0]+'}cam1:Acquire')   # initial state: started or stopped
-    ini_mode=caget(acq_pv.split('}')[0]+'}cam1:ImageMode')  # initial image mode: single [0], multiple [1], continous [2]
-    ini_expt=caget(acq_pv.split('}')[0]+'}cam1:AcquireTime') # initial exposure time
-    ini_acqperiod=caget(acq_pv.split('}')[0]+'}cam1:AcquirePeriod')  # initial acquiring period
-    ini_imnum=caget(acq_pv.split('}')[0]+'}cam1:NumImages')  # initial image number
-    
-    if acqt!='default':
+    acq_pv = session_mgr[ascan.user_detectors[0].name].pvname
+    ini_acq = caget(acq_pv.split('}')[0]+'}cam1:Acquire')   # initial state: started or stopped
+    ini_mode = caget(acq_pv.split('}')[0]+'}cam1:ImageMode')  # initial image mode: single [0], multiple [1], continous [2]
+    ini_expt = caget(acq_pv.split('}')[0]+'}cam1:AcquireTime') # initial exposure time
+    ini_acqperiod = caget(acq_pv.split('}')[0]+'}cam1:AcquirePeriod')  # initial acquiring period
+    ini_imnum = caget(acq_pv.split('}')[0]+'}cam1:NumImages')  # initial image number
+
+    if acqt != 'default':
         try:
             caput(acq_pv.split('}')[0]+'}cam1:AcquireTime',acqt)
-            print 'successfully set exposure time to [s]: ',acqt 
-        except: print 'could not set exposure time to ',acqt
+            print('successfully set exposure time to [s]: {}'.format(acqt))
+        except:
+            print('could not set exposure time to {}'.format(acqt))
     # stop camara:
     try:
         caput(acq_pv.split('}')[0]+'}cam1:Acquire',0)
-        print 'successfully stopped camera'
-    except: print 'could not stop camera'
+        print('successfully stopped camera')
+    except:
+        print('could not stop camera')
     # try to set image mode to multiple
     try:
         caput(acq_pv.split('}')[0]+'}cam1:ImageMode',1)
-        print 'successfully set ImageMode to "multiple"'
-    except: print 'could not set ImageMode to "multiple"'
-    if acqperiod!='default':
-	try:
+        print('successfully set ImageMode to "multiple"')
+    except:
+        print('could not set ImageMode to "multiple"')
+    if acqperiod != 'default':
+        try:
             caput(acq_pv.split('}')[0]+'}cam1:AcquirePeriod',acqperiod)
-            print 'successfully set acquiering period to: ',acqperiod 
-        except: print 'could not set aquireing period to ',acqperiod
+            print('successfully set acquiering period to: {}'.format(acqperiod))
+        except:
+            print('could not set aquireing period to {}'.format(acqperiod))
+
     # set number of images to be taken:
-    if imnum!='default':
+    if imnum != 'default':
         try:
-            caput(acq_pv.split('}')[0]+'}cam1:NumImages',imnum)
-            print 'successfully set number of images to: ',imnum 
-        except: print 'could not set number of images to ',imnum
-    print 'going to start the acquisition...'
+            caput(acq_pv.split('}')[0]+'}cam1:NumImages', imnum)
+            print('successfully set number of images to: {}'.format(imnum))
+        except:
+            print('could not set number of images to {}'.format(imnum))
+    print('going to start the acquisition...')
     time.sleep(1)
     # start the acquisition!!!
-    caput(acq_pv.split('}')[0]+'}cam1:ArrayCounter',0)#set Images acquired (image counter) to 0
-    
-    caput(detector.pvname.split('}')[0]+'}TIFF1:AutoSave',1)	# start auto save
-    caput(acq_pv.split('}')[0]+'}cam1:Acquire',1)		# start series acquisition
-    
+    caput(acq_pv.split('}')[0]+'}cam1:ArrayCounter',0)  # set Images acquired (image counter) to 0
+
+    caput(detector.pvname.split('}')[0]+'}TIFF1:AutoSave',1)    # start auto save
+    caput(acq_pv.split('}')[0]+'}cam1:Acquire',1)               # start series acquisition
+
     counting=0
     current_file=caget(detector.pvname.split('}')[0]+'}TIFF1:FullFileName_RBV',as_string=True)
     while counting==0:
-	time.sleep(.5)
-	if caget(acq_pv.split('}')[0]+'}cam1:ArrayCounter_RBV')==imnum: counting=1
-	if caget(detector.pvname.split('}')[0]+'}TIFF1:FullFileName_RBV',as_string=True)!=current_file:
-	  current_file=caget(detector.pvname.split('}')[0]+'}TIFF1:FullFileName_RBV',as_string=True)
-	  print 'file written: ',current_file
-	time.sleep(.1)
-
-    print 'going to stop the acquisition...'
+        time.sleep(.5)
+        if caget(acq_pv.split('}')[0]+'}cam1:ArrayCounter_RBV') == imnum:
+            counting=1
+        if caget(detector.pvname.split('}')[0]+'}TIFF1:FullFileName_RBV',as_string=True) != current_file:
+          current_file=caget(detector.pvname.split('}')[0]+'}TIFF1:FullFileName_RBV',as_string=True)
+          print('file written: {}'.format(current_file))
+        time.sleep(.1)
+
+    print('going to stop the acquisition...')
     time.sleep(.5)
-    caput(acq_pv.split('}')[0]+'}cam1:Acquire',0)		# stop series acquisition (redundent...should have stopped already
-    caput(detector.pvname.split('}')[0]+'}TIFF1:AutoSave',0)	# stop auto save
-    
-    print 'going to reset camera...'
+    caput(acq_pv.split('}')[0]+'}cam1:Acquire',0)               # stop series acquisition (redundent...should have stopped already
+    caput(detector.pvname.split('}')[0]+'}TIFF1:AutoSave',0)    # stop auto save
+
+    print('going to reset camera...')
     #time.sleep(5)
      # put camera back into initial state:
-    if acqt!='default':
+    if acqt != 'default':
         try:
             caput(acq_pv.split('}')[0]+'}cam1:AcquireTime',ini_expt)
-            print 'successfully reset exposure time to [s]: ',ini_expt 
-        except: print 'could not reset exposure time to ',ini_expt
+            print('successfully reset exposure time to [s]: {}'.format(ini_expt))
+        except:
+            print('could not reset exposure time to {}'.format(ini_expt))
     try:
-        caput(acq_pv.split('}')[0]+'}cam1:ImageMode',ini_mode)
-        print 'successfully reset ImageMode'
-    except: print 'could not reset ImageMode'
+        caput(acq_pv.split('}')[0]+'}cam1:ImageMode', ini_mode)
+        print('successfully reset ImageMode')
+    except:
+        print('could not reset ImageMode')
     try:
-        caput(acq_pv.split('}')[0]+'}cam1:Acquire',ini_acq)
-        print 'successfully reset camera acqusition mode'
-    except: print 'could not reset camera acquisition mode'
+        caput(acq_pv.split('}')[0]+'}cam1:Acquire', ini_acq)
+        print('successfully reset camera acqusition mode')
+    except:
+        print('could not reset camera acquisition mode')
     if acqperiod!='default':
         try:
-            caput(acq_pv.split('}')[0]+'}cam1:AcquirePeriod',ini_acqperiod)
-            print 'successfully reset acquisition period to [s]: ',ini_acqperiod 
-        except: print 'could not reset acquisition period  to ',ini_acqperiod
+            caput(acq_pv.split('}')[0]+'}cam1:AcquirePeriod', ini_acqperiod)
+            print('successfully reset acquisition period to [s]: {}'.format(ini_acqperiod))
+        except:
+            print('could not reset acquisition period  to {}'.format(ini_acqperiod))
     if imnum!='default':
         try:
-            caput(acq_pv.split('}')[0]+'}cam1:NumImages',ini_imnum)
-            print 'successfully reset image numbers to: ',ini_imnum 
-        except: print 'could not reset image numbers to ',ini_imnum
+            caput(acq_pv.split('}')[0]+'}cam1:NumImages', ini_imnum)
+            print('successfully reset image numbers to: {}'.format(ini_imnum))
+        except:
+            print('could not reset image numbers to {}'.format(ini_imnum))
     time.sleep(.5)
     try: 
-	caput(acq_pv.split('}')[0]+'}cam1:Acquire',ini_acq)      # restart camera if it was running before taking the series
-	print 'restarted camera'
-    except: print 'could not restart camera...'
-
-
-
-
-
+        caput(acq_pv.split('}')[0]+'}cam1:Acquire', ini_acq)      # restart camera if it was running before taking the series
+        print('restarted camera')
+    except:
+        print('could not restart camera...')
+
diff --git a/chxtools/handlers2.py b/chxtools/handlers2.py
@@ -1,7 +1,8 @@
 import numpy as np
 import h5py
 from pims import FramesSequence, Frame
-from databroker import db
+from databroker import Broker
+from .handlers import LazyEigerHandler
 
 
 class EigerImages2(FramesSequence):
@@ -96,8 +97,11 @@ def __call__(self, seq_id):
         # TODO Return a multi-dimensional PIMS seq.
         return EigerImages2(master_path, self._images_per_file, md=md)
 
-db.fs.deregister_handler('AD_EIGER')
-db.fs.deregister_handler('AD_EIGER2')
+db = Broker.named('chx')
+
+db.reg.deregister_handler('AD_EIGER')
+db.reg.deregister_handler('AD_EIGER2')
+
+db.reg.register_handler('AD_EIGER2', EigerHandler2)
+db.reg.register_handler('AD_EIGER', LazyEigerHandler)
 
-db.fs.register_handler('AD_EIGER2', EigerHandler2)
-db.fs.register_handler('AD_EIGER', LazyEigerHandler)
diff --git a/chxtools/speckle.py b/chxtools/speckle.py
@@ -10,8 +10,8 @@
 import numpy as np
 import time
 
-from skxray.core import roi
-from skxray.core.utils import bin_edges_to_centers, geometric_series
+from skbeam.core import roi
+from skbeam.core.utils import bin_edges_to_centers, geometric_series
 
 import logging
 logger = logging.getLogger(__name__)

diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,15 @@
+atom
+cython
+databroker
+enaml
+fabio
+h5py
+matplotlib
+numpy
+ophyd
+pandas
+pims
+pyepics
+scikit-beam
+scipy
+