ENH: chxtools package update for 2.0.x #16

mrakitin · 2017-12-20T01:25:46Z

Here is the updated set of files for chxtools, which now contains the updated list of dependencies which are installed during pip install. There are some outdated files, which I didn't touch, e.g.:

We should probably do something regarding handlers.py and handlers2.py. Either merge them, or use the ones from eiger-io. Ideas?

mrakitin · 2017-12-20T02:28:56Z

@yugangzhang, do you know how to fix this issue? That should be imported from somewhere.

In [4]: import chxtools.chx_utilities
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-4-16a3c9880e42> in <module>()
----> 1 import chxtools.chx_utilities

/home/xf11id/Repos/chxtools/chxtools/chx_utilities.py in <module>()
   1472     gs.TABLE_COLS = [gs.PLOT_Y]
   1473 
-> 1474 def get_ID_calibration(gapstart,gapstop,xray_eye1=xray_eye1, gapstep=.2,gapoff=0,sl=300):
   1475     """
   1476     by LW 04/20/2015

NameError: name 'xray_eye1' is not defined

You can change to
def get_ID_calibration(gapstart,gapstop,xray_eye1=None, gapstep=.2,gapoff=0,sl=300):

jrmlhermitte

Looks good. I see lots of style changes too. Was the whole document checked for flake8?

We could consider adding a flake8 checker for Travis (no tests yet).

This PR only shows a small amount of what @mrakitin had to do to get this all working. Good job looks great! :-)

jrmlhermitte · 2017-12-20T05:02:24Z

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


eventually, should be
from eiger_io.fs_handler import EigerHandler
for PIMS version
or
from eiger_io.fs_handler_dask import EigerDaskHandler
for dask version.

But let's keep it as is for now. There are some things I need to check back with Yugang on.

Just to summarize what needs to be fixed with this:

The handlers that treat the AD_EIGER and AD_EIGER2 specs should be combined into one. The only difference between the two is that the keyword argument is a different name. (Other that that API is same as far as I can tell and I've already tested this on all versions of EIGER files, of which there are four in CHX currently)

The EigerImages pims subclass (which is created by the handler per event) contains a lot of metadata which is obtained by reading from the hdf5 file directly. We should discourage that and try to make sure CHX accesses this data directly from metadatastore. Most of this data should be in a descriptor configuration. I want to discuss with Yugang and try my best to make sure we weed this out, and make a long term plan for deprecating this use.

PR here: https://github.com/NSLS-II-CHX/eiger-io/pull/8

jrmlhermitte · 2017-12-20T05:03:55Z

chxtools/handlers2.py

+db.reg.deregister_handler('AD_EIGER')
+db.reg.deregister_handler('AD_EIGER2')
+
+db.reg.register_handler('AD_EIGER2', EigerHandler2)


you could remove the previous two lines and add the overwrite=True flag to this line and bellow. Maybe we should get @danielballan 's blessing first ;-)

jrmlhermitte · 2017-12-20T05:04:37Z

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


for some history: scikit-xray was renamed to scikit-beam a while ago. So just substituting the name is perfect.

jrmlhermitte · 2017-12-20T05:04:54Z

setup.py

@@ -7,6 +7,13 @@

 from setuptools import setup, find_packages

+no_git_reqs = []


jrmlhermitte · 2017-12-20T05:09:40Z

For @mrakitin 's previous comment. Just noting that we understood that xray_eye1 is an ophyd object assumed to be in the name space. This should be changed.

jrmlhermitte · 2017-12-20T14:56:31Z

one more comment : fix the readme if you can (there are three titles)

danielballan · 2017-12-20T15:00:51Z

chxtools/handlers2.py

+db.reg.deregister_handler('AD_EIGER')
+db.reg.deregister_handler('AD_EIGER2')
+
+db.reg.register_handler('AD_EIGER2', EigerHandler2)


danielballan · 2017-12-20T15:02:26Z

chxtools/chx_wrapper.py

@@ -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


This is using very old ophyd API that definitely no longer works. It took me a minute to even remember .user_detectors; I think it goes back to the days when the RunEngine was part of ophyd and there was no such thing as plans. @mrakitin Can you open an issue to revisit this function?

danielballan · 2017-12-20T15:03:01Z

chxtools/chx_wrapper.py

@@ -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')


caget shouldn't be used in a plan. @mrakitin Can you open an issue for this too?

danielballan · 2017-12-20T15:03:23Z

chxtools/chx_wrapper.py

    # put beamline back into initial state
-    if pos_ret==True:
+    if pos_ret is True:


if pos_ret: is sufficient here.

danielballan · 2017-12-20T15:04:45Z

chxtools/chx_wrapper.py

@@ -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


session_mgr is long-gone too. I guess we should just make a note to revisit this entire file. I suspect it hasn't been used in years, so we need to decide whether to delete it or overhaul it.

yugangzhang · 2017-12-20T16:08:32Z

Great Job!

danielballan · 2017-12-20T16:14:08Z

@yugangzhang There were some comments that we had planned to address before merging here.

yugangzhang · 2017-12-20T16:44:03Z

@danielballan I think there might be some issues with handler, but it's in eiger_io package. I will revert it.

mrakitin · 2017-12-21T00:04:30Z

I implemented suggestions from @jrmlhermitte and @danielballan, see #18.

mrakitin added 8 commits December 19, 2017 18:19

ENH: chxtools enhancements for better packaging

cdcdacb

Fixed handler2.py

8acbbc1

Fix speckle.py

1a99e3c

Fix pims_readers.edf

9d3c1ec

Add pims requirements for pims_readers.eiger

ecf2131

Added final requirements for pv_explorer.run

eb2e599

Update setup.py to install requirements.txt

bef1cc1

Add missing deps (scipy and cython)

91dc6ba

mrakitin requested review from jrmlhermitte, danielballan and yugangzhang December 20, 2017 01:25

jrmlhermitte approved these changes Dec 20, 2017

View reviewed changes

danielballan reviewed Dec 20, 2017

View reviewed changes

yugangzhang merged commit 0261082 into master Dec 20, 2017

yugangzhang mentioned this pull request Dec 20, 2017

Revert "ENH: chxtools package update for 2.0.x" #17

Closed

mrakitin deleted the enh_chxtools_pkg branch December 20, 2017 22:25

This was referenced Dec 20, 2017

Revise chx_utilities.py #19

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Revise chx_wrapper.py #20

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ENH: chxtools package update for 2.0.x #16

ENH: chxtools package update for 2.0.x #16

mrakitin commented Dec 20, 2017

mrakitin commented Dec 20, 2017 •

edited by yugangzhang

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yugangzhang commented Dec 20, 2017

mrakitin commented Dec 21, 2017

		@@ -7,6 +7,13 @@

		from setuptools import setup, find_packages

		no_git_reqs = []

ENH: chxtools package update for 2.0.x #16

ENH: chxtools package update for 2.0.x #16

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mrakitin commented Dec 20, 2017

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