From 6fe99b18d29e4a69e3e17975e844b05fdb2198bc Mon Sep 17 00:00:00 2001
From: Rafael Gort <rafael.gort@xfel.eu>
Date: Thu, 7 May 2020 13:53:52 +0200
Subject: [PATCH] cleaned namespaces, collected more dssc sub-methods, not
tested
---
src/toolbox_scs/__init__.py | 24 +++++++
src/toolbox_scs/detectors/LICENSE_BSD | 30 ++++++++
src/toolbox_scs/detectors/__init__.py | 32 ++++++++-
.../azimuthal_integrator.py | 21 +++---
src/toolbox_scs/detectors/dssc.py | 29 ++++++--
src/toolbox_scs/detectors/dssc_plot.py | 5 +-
src/toolbox_scs/detectors/dssc_routines.py | 70 ++++++++++++++++---
src/toolbox_scs/misc/__init__.py | 2 -
8 files changed, 183 insertions(+), 30 deletions(-)
create mode 100644 src/toolbox_scs/detectors/LICENSE_BSD
rename src/toolbox_scs/{misc => detectors}/azimuthal_integrator.py (85%)
diff --git a/src/toolbox_scs/__init__.py b/src/toolbox_scs/__init__.py
index 5b2cc72..1ce1e6c 100644
--- a/src/toolbox_scs/__init__.py
+++ b/src/toolbox_scs/__init__.py
@@ -14,3 +14,27 @@ __all__ = (
# Variables
"mnemonics",
)
+
+
+# ------------------------------------------------------------------------------
+# Clean namespace
+# ------------------------------------------------------------------------------
+
+# items to avoid
+clean_ns = [
+ # filenames
+ 'load',
+ 'constants',
+ # folders
+ 'misc',
+ 'util',
+ 'detectors',
+ 'routines',
+ ]
+
+for name in dir():
+ if name in clean_ns:
+ del globals()[name]
+
+del globals()['clean_ns']
+del globals()['name']
\ No newline at end of file
diff --git a/src/toolbox_scs/detectors/LICENSE_BSD b/src/toolbox_scs/detectors/LICENSE_BSD
new file mode 100644
index 0000000..def0969
--- /dev/null
+++ b/src/toolbox_scs/detectors/LICENSE_BSD
@@ -0,0 +1,30 @@
+BSD 3-Clause License
+
+Copyright (c) 2019, Michael Schneider
+Copyright (c) 2020, SCS-team
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+ contributors may be used to endorse or promote products derived from
+ this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
\ No newline at end of file
diff --git a/src/toolbox_scs/detectors/__init__.py b/src/toolbox_scs/detectors/__init__.py
index 4890887..abb5916 100644
--- a/src/toolbox_scs/detectors/__init__.py
+++ b/src/toolbox_scs/detectors/__init__.py
@@ -18,6 +18,36 @@ __all__ = (
"process_intra_train",
"split_frames",
# Classes
- DSSC
+ "DSSC"
# Variables
)
+
+
+# -----------------------------------------------------------------------------
+# Clean namespace
+# -> certain filenames we dont need in the namespace. Especially not those
+# that are marked as private by using an underscore (_<filename>.py).
+# -----------------------------------------------------------------------------
+
+# items to avoid
+clean_ns = [
+ # filenames
+ 'DSSC_bkp',
+ 'DSSC1module',
+ 'dssc',
+ 'dssc_routines',
+ 'dssc_data',
+ 'dssc_plot',
+ 'azimuthal_integrator',
+ 'FastCCD',
+ 'tim',
+ 'xgm',
+ ]
+
+
+for name in dir():
+ if name in clean_ns:
+ del globals()[name]
+
+del globals()['clean_ns']
+del globals()['name']
diff --git a/src/toolbox_scs/misc/azimuthal_integrator.py b/src/toolbox_scs/detectors/azimuthal_integrator.py
similarity index 85%
rename from src/toolbox_scs/misc/azimuthal_integrator.py
rename to src/toolbox_scs/detectors/azimuthal_integrator.py
index e682281..56759ac 100644
--- a/src/toolbox_scs/misc/azimuthal_integrator.py
+++ b/src/toolbox_scs/detectors/azimuthal_integrator.py
@@ -3,9 +3,9 @@ import numpy as np
class AzimutalIntegrator(object):
def __init__(self, imageshape, center, polar_range, dr=2, aspect=204/236):
'''
- Create a reusable integrator for repeated azimuthal integration of similar
- images. Calculates array indices for a given parameter set that allows
- fast recalculation.
+ Create a reusable integrator for repeated azimuthal integration of
+ similar images. Calculates array indices for a given parameter set that
+ allows fast recalculation.
Parameters
==========
@@ -16,10 +16,12 @@ class AzimutalIntegrator(object):
center coordinates in pixels
polar_range : tuple of ints
- start and stop polar angle (in degrees) to restrict integration to wedges
+ start and stop polar angle (in degrees) to restrict integration to
+ wedges
dr : int, default 2
- radial width of the integration slices. Takes non-square DSSC pixels into account.
+ radial width of the integration slices. Takes non-square DSSC
+ pixels into account.
aspect: float, default 204/236 for DSSC
aspect ratio of the pixel pitch
@@ -46,7 +48,8 @@ class AzimutalIntegrator(object):
# array of polar angles
if np.abs(polar_range[1]-polar_range[0]) > 180:
- raise ValueError('Integration angle too wide, should be within 180 degrees')
+ raise ValueError('Integration angle too wide, should be within 180'
+ ' degrees')
if np.abs(polar_range[1]-polar_range[0]) < 1e-6:
raise ValueError('Integration angle too narrow')
@@ -64,11 +67,13 @@ class AzimutalIntegrator(object):
self.distance = np.array([])
self.flat_indices = []
for dist in range(dr, self.maxdist, dr):
- ring_mask = self.polar_mask * (dist_array >= (dist - dr)) * (dist_array < dist)
+ ring_mask = self.polar_mask * (dist_array >= (dist - dr)) * \
+ (dist_array < dist)
self.flat_indices.append(self.index_array[ring_mask])
self.distance = np.append(self.distance, dist)
def __call__(self, image):
assert self.shape == image.shape, 'image shape does not match'
image_flat = image.flatten()
- return np.array([np.nansum(image_flat[indices]) for indices in self.flat_indices])
+ return np.array([np.nansum(image_flat[indices]) \
+ for indices in self.flat_indices])
diff --git a/src/toolbox_scs/detectors/dssc.py b/src/toolbox_scs/detectors/dssc.py
index 43d0927..09a608e 100644
--- a/src/toolbox_scs/detectors/dssc.py
+++ b/src/toolbox_scs/detectors/dssc.py
@@ -1,9 +1,26 @@
+"""
+ DSSC-detector class module
+ --------------------------
+
+ The dssc detector class provides a namespace for frequent evaluation
+ routines.
+
+ comments:
+ - DSSC class methods will mostly use functions defined in other
+ files. The redefinition of its names makes it easy to adapt the code in
+ case we later rename the underlying functions in the course of
+ development.
+ - contributions should comply with pep8 code structure guidelines.
+"""
+
from .dssc_routines import (
- load_dssc_info as dssc_info,
- calc_xgm_frame_indices as xgm_frame_indices
-)
-from .dssc_data import save_to_file, load_from_file
-from .dssc_plot import xgm_threshold
+ load_dssc_info as _dssc_info,
+ calc_xgm_frame_indices as _xgm_frame_indices
+ )
+from .dssc_data import (
+ save_to_file as _save_to_file,
+ load_from_file as _load_from_file,
+ )
class DSSC:
@@ -12,7 +29,7 @@ class DSSC:
pass
def __del__(self):
- # cleanup_dir()
+ # cleanup
pass
# -------------------------------------------------------------------------
diff --git a/src/toolbox_scs/detectors/dssc_plot.py b/src/toolbox_scs/detectors/dssc_plot.py
index bd9789f..c0ec8b3 100644
--- a/src/toolbox_scs/detectors/dssc_plot.py
+++ b/src/toolbox_scs/detectors/dssc_plot.py
@@ -3,7 +3,7 @@
Plotting sub-routines frequently done in combination with dssc analysis.
The initial code is based on: https://github.com/dscran/dssc_process
/blob/master/example_image_process_pulsemask.ipynb
-
+
Todo: For visualization of statistical information we could eventually
switch to seaborn: https://seaborn.pydata.org/
"""
@@ -15,7 +15,6 @@ import numpy as np
import xarray as xr
-
def xgm_threshold(xgm, scan,
xgm_min = None, xgm_max = None,
run_nr = '',
@@ -61,4 +60,4 @@ def trains_per_step(scan,
if safe_fig == True:
tstamp = strftime('%y%m%d_%H%M')
- fig.savefig(f'images/run{run_nr}_scan_{tstamp}.png', dpi=200)
\ No newline at end of file
+ fig.savefig(f'images/run{run_nr}_scan_{tstamp}.png', dpi=200)
diff --git a/src/toolbox_scs/detectors/dssc_routines.py b/src/toolbox_scs/detectors/dssc_routines.py
index cc16436..ded1405 100644
--- a/src/toolbox_scs/detectors/dssc_routines.py
+++ b/src/toolbox_scs/detectors/dssc_routines.py
@@ -1,15 +1,13 @@
-# -*- coding: utf-8 -*-
-'''
-@author: Michael Schneider, with input from XFEL-CAS and SCS beamline staff
+"""
+ DSSC-related sub-routines.
-karabo_data: https://github.com/European-XFEL/karabo_data
-SCS ToolBox: https://git.xfel.eu/gitlab/SCS/ToolBox
+ original-author: Michael Schneider
+ authors: SCS-team members
+
+ license: BSD 3-Clause License (see LICENSE_BSD for more info)
-contributions should comply with pep8 code structure guidelines.
-
-Copyright (c) 2019, Michael Schneider
-All rights reserved.
-'''
+ comment: contributions should comply with pep8 code structure guidelines.
+"""
import logging
from tqdm import tqdm
@@ -47,12 +45,46 @@ def load_dssc_info(proposal, run_nr):
return info
+def load_geom(geopath=None, quad_pos=None):
+ """
+ Loads and return the DSSC geometry.
+
+ Parameters
+ ----------
+ geopath: str
+ path to the h5 geometry file. If None uses a default file.
+ quad_pos: list of quadrants tuple position. If None uses a default
+ position.
+
+ Returns
+ -------
+ geom: extra_geom.DSSC_1MGeometry
+ loaded geometry object
+ """
+ if quad_pos is None:
+ quad_pos = [(-124.100, 3.112), # TR
+ (-133.068, -110.604), # BR
+ ( 0.988, -125.236), # BL
+ ( 4.528, -4.912) # TL
+ ]
+
+ if geopath is None:
+ geopath = '/gpfs/exfel/sw/software/git/EXtra-geom/' \
+ 'docs/dssc_geo_june19.h5'
+
+ geom = DSSC_1MGeometry.from_h5_file_and_quad_positions(geopath, quad_pos)
+ return geom
+
+
def calc_xgm_frame_indices(nbunches, framepattern):
"""
Returns a coordinate array for XGM data. The coordinates correspond to
DSSC frame numbers and depend on the number of FEL pulses per train
("nbunches") and the framepattern. In framepattern, dark DSSC frame
names (i.e., without FEL pulse) _must_ include "dark" as a substring.
+
+ Copyright (c) 2019, Michael Schneider
+ Copyright (c) 2020, SCS-team
Parameters
----------
@@ -85,6 +117,9 @@ def prepare_module_empty(scan_variable, framepattern):
"""
Create empty (zero-valued) DataArray for a single DSSC module
to iteratively add data to.
+
+ Copyright (c) 2019, Michael Schneider
+ Copyright (c) 2020, SCS-team
Parameters
----------
@@ -123,6 +158,9 @@ def load_chunk_data(sel, sourcename, maxframes=None):
"""
Load selected DSSC data. The flattened multi-index (trains+pulses) is
unraveled before returning the data.
+
+ Copyright (c) 2019, Michael Schneider
+ Copyright (c) 2020, SCS-team
Parameters
----------
@@ -162,6 +200,9 @@ def merge_chunk_data(module_data, chunk_data, framepattern):
['pumped', 'unpumped', 'sum_count']
Concatenates the data along a new dimension ('tmp') and uses
the sum() method for automatic dtype conversion
+
+ Copyright (c) 2019, Michael Schneider
+ Copyright (c) 2020, SCS-team
Parameters
----------
@@ -194,6 +235,9 @@ def split_frames(data, pattern, prefix=''):
"""
Split frames according to "pattern" (possibly repeating) and average over
resulting splits.
+
+ Copyright (c) 2019, Michael Schneider
+ Copyright (c) 2020, SCS-team
Parameters
----------
@@ -224,6 +268,9 @@ def process_intra_train(job):
"""
Aggregate DSSC data (chunked, to fit into memory) for a single module.
Averages over all trains, but keeps all pulses.
+
+ Copyright (c) 2019, Michael Schneider
+ Copyright (c) 2020, SCS-team
Parameters
----------
@@ -304,6 +351,9 @@ def process_dssc_module(job):
Groups by "scan_variable" in given scanfile - use dummy scan_variable to
average over all trains. This implies, that only trains found in the
scanfile are considered.
+
+ Copyright (c) 2019, Michael Schneider
+ Copyright (c) 2020, SCS-team
Parameters
----------
diff --git a/src/toolbox_scs/misc/__init__.py b/src/toolbox_scs/misc/__init__.py
index 00256d1..9afb2d9 100644
--- a/src/toolbox_scs/misc/__init__.py
+++ b/src/toolbox_scs/misc/__init__.py
@@ -3,7 +3,6 @@ from .bunch_pattern import (extractBunchPattern, pulsePatternInfo,
)
from .bunch_pattern_external import is_sase_3, is_sase_1, is_ppl
from .laser_utils import positionToDelay, degToRelPower
-from .azimuthal_integrator import AzimutalIntegrator
__all__ = (
@@ -21,6 +20,5 @@ __all__ = (
"positionToDelay",
"degToRelPower",
# Classes
- "AzimutalIntegrator",
# Variables
)
--
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