Commit 5cdbfc0b authored by Damien Naudet's avatar Damien Naudet
Browse files

Refactored merge.

parent 2496cb20
......@@ -28,10 +28,9 @@ __authors__ = ["D. Naudet"]
__date__ = "20/04/2016"
__license__ = "MIT"
import os
import time
from xsocs.util.id01_spec import merge_scan_data
from xsocs.process.merge import merge_scan_data
# output directory (some temporary files will also be written there)
output_dir = '/path/to/output/'
......@@ -64,6 +63,12 @@ scan_ids = None
# number, while in version 1 we pad the value to to 5 digits)
version = 1
# you can also set the offset and padding with the nr_offset and nr_padding
# keywords to the merge_scan_data function, or ignore them if you want
# to use the default values specified by "version".
# nr_offset = -1
# nr_padding = 4
# channels (pix.) per degree (used by xrayutilities when converting to
# qspace coordinates)
# (not that this value can also be changed later when calling the
......@@ -73,12 +78,6 @@ chan_per_deg = [318., 318.]
# direct beam position in the detector coordinates
center_chan = [140, 322]
# the merge will actually create one file per scan, then a "master" file
# (in the output directory) that will contain links to those files. You can
# give the master file the name you want (if None, a name will be generated
# with the prefix found in the spec file)
master_f = None
# checks if some of the output files already exist
# set it to True if you dont care about overwriting files
overwrite = False
......@@ -86,15 +85,14 @@ overwrite = False
t_merge = time.time()
merge_scan_data(output_dir,
spec_f,
beam_energy=beam_energy,
chan_per_deg=chan_per_deg,
center_chan=center_chan,
scan_ids=scan_ids,
master_f=master_f,
img_dir=img_base,
version=version,
overwrite=overwrite)
spec_f,
beam_energy=beam_energy,
chan_per_deg=chan_per_deg,
center_chan=center_chan,
scan_ids=scan_ids,
img_dir=img_base,
version=version,
overwrite=overwrite)
t_merge = time.time() - t_merge
print('Total time spent : {0}'.format(t_merge))
......@@ -35,7 +35,8 @@ import shutil
from types import MethodType
from functools import partial
from ...util.id01_spec import Id01DataMerger
from ...process.merge import KmapSpecParser, KmapMerger
from ..widgets.AcqParamsWidget import AcqParamsWidget
from ..widgets.Input import StyledLineEdit
......@@ -210,7 +211,7 @@ class _ScansSelectDialog(Qt.QDialog):
item = self.__table_widget.item(row, self.SEL_COL)
item.setCheckState(Qt.Qt.Unchecked)
def __showMore(self, *args, **kwargs):
def __showMore(self):
if self.__more_bn.text() == 'More':
self.__more_bn.setText('Less')
hide = False
......@@ -286,7 +287,7 @@ class _ScansInfoDialog(Qt.QDialog):
class _MergeProcessDialog(Qt.QDialog):
__sigMergeDone = Qt.Signal(object)
__sigMergeDone = Qt.Signal()
def __init__(self, merger, **kwargs):
super(_MergeProcessDialog, self).__init__(**kwargs)
......@@ -351,7 +352,7 @@ class _MergeProcessDialog(Qt.QDialog):
self.__merger = merger
self.__status = False
def __onAccept(self, *args, **kwargs):
def __onAccept(self):
merger = self.__merger
warn = merger.check_overwrite()
......@@ -383,7 +384,7 @@ class _MergeProcessDialog(Qt.QDialog):
self.__time = time.time()
def __onAbort(self, *args, **kwargs):
def __onAbort(self):
abort_diag = Qt.QMessageBox(Qt.QMessageBox.Information,
'Aborting...',
'<b>Cancelling merge.</b>'
......@@ -394,11 +395,11 @@ class _MergeProcessDialog(Qt.QDialog):
abort_diag.setAttribute(Qt.Qt.WA_DeleteOnClose)
abort_diag.setStandardButtons(Qt.QMessageBox.NoButton)
abort_diag.show()
self.__merger.abort_merge(wait=False)
self.__merger.abort(wait=False)
def __mergeDone(self, result):
def __mergeDone(self):
print('TOTAL : {0}.'.format(time.time() - self.__time))
self.__status = result[0]
self.__status = self.__merger.status
self.__qtimer.stop()
self.__qtimer = None
self.__onProgress()
......@@ -412,8 +413,8 @@ class _MergeProcessDialog(Qt.QDialog):
else:
self.__bn_box.rejected.connect(self.reject)
def __onProgress(self, *args, **kwargs):
progress = self.__merger.merge_progress()
def __onProgress(self):
progress = self.__merger.progress()
if progress is None:
return
tree_wid = self.__tree_widget
......@@ -443,7 +444,7 @@ class MergeWidget(Qt.QDialog):
'offset': [-1, 0]}
_defaultVersion = 1
__sigParseDone = Qt.Signal()
__sigParsed = Qt.Signal()
def __init__(self,
spec_file=None,
......@@ -748,6 +749,7 @@ class MergeWidget(Qt.QDialog):
parseBn.setEnabled(False)
self.__merger = None
self.__parser = None
self.info_wid = None
if tmp_dir is None:
......@@ -768,8 +770,6 @@ class MergeWidget(Qt.QDialog):
print('Using temporary folder : {0}.'.format(tmp_dir))
self.__sigParseDone.connect(self.__parseSpecDone)
self.__widgetIsSetup = False
self.__xsocs_h5 = None
......@@ -780,6 +780,8 @@ class MergeWidget(Qt.QDialog):
self.__resetState()
self.__sigParsed.connect(self.__slotParsed, Qt.Qt.QueuedConnection)
def showEvent(self, *args, **kwargs):
if not self.__widgetIsSetup:
self.__widgetIsSetup = True
......@@ -887,15 +889,15 @@ class MergeWidget(Qt.QDialog):
name = 'Prefix'
prefix = self.__output['prefix']
if len(prefix) == 0:
if not prefix:
raise ValueError('parameter is mandatory.')
merger.prefix = prefix
merger.prefix = str(prefix)
name = 'Output directory'
outDir = self.__output['outdir']
if len(outDir) == 0:
if not outDir:
raise ValueError('parameter is mandatory.')
merger.output_dir = outDir
merger.output_dir = str(outDir)
except Exception as ex:
Qt.QMessageBox.critical(self, 'Error',
......@@ -917,15 +919,16 @@ class MergeWidget(Qt.QDialog):
process_diag = _MergeProcessDialog(merger, parent=self)
process_diag.setAttribute(Qt.Qt.WA_DeleteOnClose)
process_diag.accepted.connect(partial(self.__mergeDone, status=True))
process_diag.rejected.connect(partial(self.__mergeDone, status=False))
process_diag.accepted.connect(partial(self.__mergeDone))
process_diag.rejected.connect(partial(self.__mergeDone))
process_diag.setModal(True)
self.__process_diag = process_diag
process_diag.show()
def __mergeDone(self, status):
def __mergeDone(self):
self.__process_diag = None
if status:
status = self.__merger.status
if status == KmapMerger.DONE:
self.__xsocs_h5 = self.__merger.master_file
self.accept()
......@@ -1025,7 +1028,7 @@ class MergeWidget(Qt.QDialog):
if merger is None:
enable = False
else:
enable = merger.parsed and len(merger.matched_ids) > 0
enable = len(merger.matched_ids) > 0
self.__outputGbx.setEnabled(enable)
if not enable:
......@@ -1067,20 +1070,16 @@ class MergeWidget(Qt.QDialog):
padding = self.__input['padding']
offset = self.__input['offset']
spec_h5 = os.path.join(self.__tmp_dir_merge, 'temp_spec.h5')
try:
if self.__merger is None:
self.__merger = Id01DataMerger(specFile,
self.__tmp_dir_merge,
img_dir=imgDir,
# version=version,
nr_offset=offset,
nr_padding=padding)
else:
self.__merger.reset(str(specFile),
img_dir=imgDir,
# version=version,
nr_offset=offset,
nr_padding=padding)
self.__parser = KmapSpecParser(specFile,
spec_h5,
img_dir=imgDir,
# version=version,
nr_offset=offset,
nr_padding=padding,
callback=self.__sigParsed.emit)
except Exception as ex:
msg = ('Parsing failed: {0}.\n'
'Message : {1}.'
......@@ -1104,10 +1103,9 @@ class MergeWidget(Qt.QDialog):
info_wid.setStandardButtons(Qt.QMessageBox.NoButton)
info_wid.show()
self.info_wid = info_wid
self.__merger.parse(blocking=False,
callback=self.__sigParseDone.emit)
self.__parser.parse(blocking=False)
def __parseSpecDone(self, *args, **kwargs):
def __slotParsed(self):
self.info_wid.done(0)
self.info_wid = None
......@@ -1115,6 +1113,15 @@ class MergeWidget(Qt.QDialog):
self.__parseBn.setEnabled(True)
self.__parseBn.setText('Parse file.')
self.__merger = KmapMerger(self.__parser.results.spec_h5,
self.__parser.results,
output_dir=self.__output['outdir'])
self.__output['prefix'] = self.__merger.prefix
blocked = self.__prefixEdit.blockSignals(True)
self.__prefixEdit.setText(self.__merger.prefix)
self.__prefixEdit.blockSignals(blocked)
self.__updateScansInfos()
self.__updateOutputGroupBox()
......@@ -1137,7 +1144,7 @@ class MergeWidget(Qt.QDialog):
selected_ids = merger.selected_ids
no_match_ids = merger.no_match_ids
no_img_ids = merger.no_img_ids
enable = merger.parsed
enable = True
prefix = merger.prefix
nTotal = len(matched_ids)
......
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#!/usr/bin/python
# coding: utf8
# /*##########################################################################
#
# Copyright (c) 2015-2016 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# ###########################################################################*/
__authors__ = ["D. Naudet"]
__date__ = "20/04/2016"
__license__ = "MIT"
import re
import glob
import os.path
from collections import namedtuple
from threading import Thread
import h5py
from silx.io import spectoh5
# regular expression matching the imageFile comment line
_IMAGEFILE_LINE_PATTERN = ('^#C imageFile '
'dir\[(?P<dir>[^\]]*)\] '
'prefix\[(?P<prefix>[^\]]*)\] '
'(idxFmt\[(?P<idxFmt>[^\]]*)\] ){0,1}'
'nextNr\[(?P<nextNr>[^\]]*)\] '
'suffix\[(?P<suffix>[^\]]*)\]$')
# #######################################################################
# #######################################################################
KmapParseResults = namedtuple('KmapParseResults',
['img_info', 'no_img_info', 'error', 'spec_h5'])
KmapMatchResults = namedtuple('KmapMatchResults',
['matched', 'not_matched',
'no_img_info', 'error',
'spec_h5'])
# #######################################################################
# #######################################################################
class KmapSpecParser(object):
(READY, RUNNING, DONE,
ERROR, CANCELED, UNKNOWN) = __STATUSES = range(6)
""" Available status codes """
status = property(lambda self: self.__status)
""" Current status code of this instance """
statusMsg = property(lambda self: self.__status_msg)
""" Status message if any, or None """
results = property(lambda self: self.__results)
""" Parse results. KmapParseResults instance. """
def __init__(self,
spec_fname,
spec_h5,
img_dir=None,
version=1,
nr_padding=None,
nr_offset=None,
callback=None):
"""
Parser for the Kmap SPEC files. This loads a spec file, converts
it to HDF5 and then tries to match scans and edf image files.
:param spec_fname: Path to the spec file.
:param spec_h5: Name of the HDF5 file that will be created and filled
with the contents of the SPEC file
.. seealso : silx.io.convert_spec_h5.convert
:param img_dir: directory where the images are stored, if they are not
stored where the path (#C imageFile line) in the SPEC file points to.
:param version: version of the spec file. It is currently used to get
the offset and padding to apply to the nextNr value found in the
spec scan headers. This nextNr is then used to generate the image
file name. Set it to 0 if you are merging data generated
before April 2016 (TBC).
:param nr_padding: zero padding to apply to the nextNr number found
in the SPEC file.
:param nr_offset: offset to apply to the nextNr number found
in the SPEC file.
:param callback: callback to call when the parsing is done
"""
super(KmapSpecParser, self).__init__()
self.__status = None
self.__set_status(self.UNKNOWN, 'Init')
self.__results = None
self.__thread = None
self.__spec_fname = spec_fname
self.__spec_h5 = spec_h5
self.__callback = callback
self.__img_dir = img_dir
self.__version = version
self.__nr_padding = nr_padding
self.__nr_offset = nr_offset
self.__set_status(self.READY)
def __set_status(self, status, msg=None):
"""
Sets the status of this instance.
:param status:
:param msg:
:return:
"""
assert status in self.__STATUSES
self.__status = status
self.__status_msg = msg
def parse(self, blocking=True):
"""
Starts the parsing.
:param blocking: if False, the parsing will be done in a separate
thread and this method will return immediately.
:return:
"""
if self.__thread and self.__thread.is_alive():
raise RuntimeError('This KmapSpecParser instance is already '
'parsing.')
self.__results = None
if blocking:
self.__run_parse()
if self.__callback:
self.__callback()
else:
thread = self.__thread = Thread(target=self.__run_parse)
thread.start()
def __run_parse(self):
"""
Runs the parsing.
:return:
"""
self.__set_status(self.RUNNING)
try:
_spec_to_h5(self.__spec_fname, self.__spec_h5)
self.__results = _find_scan_img_files(self.__spec_h5,
img_dir=self.__img_dir,
version=self.__version,
nr_padding=self.__nr_padding,
nr_offset=self.__nr_offset)
self.__set_status(self.DONE)
except Exception as ex:
self.__set_status(self.ERROR, str(ex))
# TODO : catch exception?
if self.__callback:
self.__callback()
return self.__results
def wait(self):
"""
Waits until parsing is done, or returns if it is not running.
:return:
"""
if self.__thread:
self.__thread.join()
# #######################################################################
# #######################################################################
def _spec_to_h5(spec_filename, h5_filename):
"""
Converts a spec file into a HDF5 file.
:param spec_filename: name of the spec file to convert to HDF5.
:type spec_filename: str
:param h5_filename: name of the HDF5 file to create.
:type h5_filename: str
.. seealso : silx.io.convert_spec_h5.convert
"""
spectoh5.convert(spec_filename,
h5_filename,
mode='w')
# ########################################################################
# ########################################################################
def _spec_get_img_filenames(spec_h5_filename):
"""
Parsed spec scans headers to retrieve the associated image files.
:param spec_h5_filename: name of the HDF5 file containing spec data.
:type spec_h5_filename: str
.. todo : can we suppose that there's
only one scan per scan number?
i.e : no 0.2, 1.2, ...
.. todo : expecting only one imageFile comment line per scan. Is this
always true?
:return: 3 elements tuple : a dict containing the scans that have valid
image file info, a list with the scans that dont have any image files,
and a list of the scans that have more that one image files.
:rtype: *list* (*dict*, *list*, *list*)
"""
with h5py.File(spec_h5_filename, 'r') as h5_f:
# scans for which a file name was found
with_file = {}
# scans for which no file name was found
without_file = []
# scans for which more than one file name was found
# -> this case is not expected/handled atm
error_scans = []
# regular expression to find the imagefile line
regx = re.compile(_IMAGEFILE_LINE_PATTERN)
for k_scan, v_scan in h5_f.items():
header = v_scan['instrument/specfile/scan_header'][()]
header = header.decode().split('\n')
imgfile_match = [m for line in header
if line.startswith('#C imageFile')
for m in [regx.match(line.strip())] if m]
# TODO : provide some more info
# expecting only one imagefile line per scan
if len(imgfile_match) > 1:
error_scans.append(k_scan)
continue
# if no imagefile line
if len(imgfile_match) == 0:
without_file.append(k_scan)
continue
# extracting the named subgroups
imgfile_grpdict = imgfile_match[0].groupdict()
with_file[k_scan] = imgfile_grpdict
return KmapParseResults(img_info=with_file,
no_img_info=without_file,
error=error_scans,
spec_h5=spec_h5_filename)
# ########################################################################
# ########################################################################
def _find_scan_img_files(spec_h5_filename,
img_dir=None,
version=1,
nr_padding=None,
nr_offset=None):
"""
Parses the provided "*spec*" HDF5 file and tries to find the edf file
associated with each scans. will look for the files in img_dir if
provided (instead of looking for the files in the path written
in the spec file).
:param spec_h5_filename: name of the HDF5 file containing spec data.
:type spec_h5_filename: str
:param img_dir: directory path. If provided the image files will be
looked for into that folder instead of the one found in the scan
headers.
:type img_dir: *optional* str
:param version: version of the spec file. It is currently used to get
the offset and padding to apply to the nextNr value found in the spec scan
headers. This nextNr is then used to generate the image file name. Set it
to 0 if you are merging data generated before April 2016 (TBC).
:type img_dir: *optional* int
:returns: 4 elements tuple : a dict containing the scans whose image file
has been found, a dict containing the scans that have that have
valid image file info in the scan header but whose image file has not
been found, a list with the scans that dont have any image file info,
and a list of the scans that have more that one image file info line.
:rtype: *list* (*dict*, *dict*, *list*, *list*)
"""
if img_dir and not os.path.exists(img_dir):
raise ValueError('Image folder not found : {0}'
''.format(img_dir))
imgfile_info = _spec_get_img_filenames(spec_h5_filename)
with_files = imgfile_info.img_info
complete_scans = {}
incomplete_scans = {}
if version == 0:
nextnr_ofst = -1
nextnr_pattern = '{0:0>4}'
else:
nextnr_ofst = 0
nextnr_pattern = '{0:0>5}'
if nr_padding is not None: