diff --git a/cfel_fabio.py b/cfel_fabio.py
new file mode 100644
index 0000000000000000000000000000000000000000..7edc689eab8b36da91ad536a790858df059a0d9b
--- /dev/null
+++ b/cfel_fabio.py
@@ -0,0 +1,88 @@
+# This file is part of cfelpyutils.
+#
+# cfelpyutils is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# cfelpyutils is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with cfelpyutils. If not, see <http://www.gnu.org/licenses/>.
+"""
+Utilities based on the fabio python module.
+
+This module contains utilities based on the fabio python module.
+files.
+"""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+
+import numpy
+import fabio.cbfimage
+
+
+def read_cbf_from_stream(stream):
+ """Reads a cbfimage object out of a data string buffer.
+
+ Read a data string buffer received as a payload from the PETRAIII P11 sender, and creates a cbfimage object from
+ it (See the documentation of the fabio python module).
+
+ Args:
+
+ stream (str): a data string buffer received from the PETRAIII P11 sender.
+
+ Returns:
+
+ cbf_obj (fabio.cbfimage): a cbfimage object containing the data extracted
+ from the string buffer.
+ """
+
+ cbf_obj = fabio.cbfimage.cbfimage()
+
+ cbf_obj.header = {}
+ cbf_obj.resetvals()
+
+ infile = stream
+ cbf_obj._readheader(infile)
+ if fabio.cbfimage.CIF_BINARY_BLOCK_KEY not in cbf_obj.cif:
+ err = "Not key %s in CIF, no CBF image in stream" % fabio.cbfimage.CIF_BINARY_BLOCK_KEY
+ logger.error(err)
+ for kv in cbf_obj.cif.items():
+ print("%s: %s" % kv)
+ raise RuntimeError(err)
+ if cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY] == "CIF Binary Section":
+ cbf_obj.cbs += infile.read(len(fabio.cbfimage.STARTER) + int(cbf_obj.header["X-Binary-Size"])
+ - len(cbf_obj.cbs) + cbf_obj.start_binary)
+ else:
+ if len(cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY]) > int(
+ cbf_obj.header["X-Binary-Size"]) + cbf_obj.start_binary + len(fabio.cbfimage.STARTER):
+ cbf_obj.cbs = cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY][:int(cbf_obj.header["X-Binary-Size"]) +
+ cbf_obj.start_binary +
+ len(fabio.cbfimage.STARTER)]
+ else:
+ cbf_obj.cbs = cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY]
+ binary_data = cbf_obj.cbs[cbf_obj.start_binary + len(fabio.cbfimage.STARTER):]
+
+ if "Content-MD5" in cbf_obj.header:
+ ref = numpy.string_(cbf_obj.header["Content-MD5"])
+ obt = fabio.cbfimage.md5sum(binary_data)
+ if ref != obt:
+ logger.error("Checksum of binary data mismatch: expected %s, got %s" % (ref, obt))
+
+ if cbf_obj.header["conversions"] == "x-CBF_BYTE_OFFSET":
+ cbf_obj.data = cbf_obj._readbinary_byte_offset(binary_data).astype(cbf_obj.bytecode).reshape(
+ (cbf_obj.dim2, cbf_obj.dim1))
+ else:
+ raise Exception(IOError, "Compression scheme not yet supported, please contact the author")
+
+ cbf_obj.resetvals()
+ # ensure the PIL image is reset
+ cbf_obj.pilimage = None
+ return cbf_obj
diff --git a/cfelgeom.py b/cfel_geom.py
similarity index 73%
rename from cfelgeom.py
rename to cfel_geom.py
index 9711c1b8b085381dd43f2519a3571167f33701f2..0f5937e69ceded764be1da63bd84ad6a8e9f6acf 100644
--- a/cfelgeom.py
+++ b/cfel_geom.py
@@ -19,15 +19,20 @@ This module contains utilities for the processing of CrystFEL-style geometry
files.
"""
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
import numpy
def apply_geometry_from_file(data_as_slab, geometry_filename):
- """Parse a geometry file and applies the geometry to detector data in 'slab' format.
- Turns a 2d array of pixel values into an array containing a representation of the
- physical layout of the detector, keeping the origin of the reference system at the
- beam interaction point.
+ """Parses a geometry file and applies the geometry to data.
+
+ Parses a geometry file and applies the geometry to detector data in 'slab' format. Turns a 2d array of pixel
+ values into an array containing a representation of the physical layout of the detector, keeping the origin of
+ the reference system at the beam interaction point.
Args:
@@ -37,9 +42,8 @@ def apply_geometry_from_file(data_as_slab, geometry_filename):
Returns:
- im_out (numpy.ndarray data_as_slab.dtype): Array containing a representation of the
- physical layout of the detector, with the origin of the reference system at the
- beam interaction point.
+ im_out (numpy.ndarray data_as_slab.dtype): Array containing a representation of the physical layout of the
+ detector, with the origin of the reference system at the beam interaction point.
"""
yx, slab_shape, img_shape = pixel_maps_for_image_view(geometry_filename)
@@ -50,10 +54,11 @@ def apply_geometry_from_file(data_as_slab, geometry_filename):
def apply_geometry_from_pixel_maps(data_as_slab, yx, im_out=None):
- """Applies geometry, in the form of pixel maps, to detector data in 'slab' format.
- Turns a 2d array of pixel values into an array containing a representation of the
- physical layout of the detector, keeping the origin of the reference system at the
- beam interaction point.
+ """Applies geometry in pixel map format to data.
+
+ Applies geometry, in the form of pixel maps, to detector data in 'slab' format. Turns a 2d array of pixel values
+ into an array containing a representation of the physical layout of the detector, keeping the origin of the
+ reference system at the beam interaction point.
Args:
@@ -61,15 +66,15 @@ def apply_geometry_from_pixel_maps(data_as_slab, yx, im_out=None):
yx (tuple): the yx pixel maps describing the geometry of the detector; each map is a numpy.ndarray.
- im_out (Optional[numpy.ndarray]): array to hold the output; if not provided, one will be generated automatically.
-
+ im_out (Optional[numpy.ndarray]): array to hold the output; if not provided, one will be generated
+ automatically.
Returns:
- im_out (numpy.ndarray data_as_slab.dtype): Array containing a representation of the
- physical layout of the detector, with the origin of the reference system at the
- beam interaction point.
+ im_out (numpy.ndarray data_as_slab.dtype): Array containing a representation of the physical layout of the
+ detector, with the origin of the reference system at the beam interaction point.
"""
+
if im_out is None:
im_out = numpy.zeros(data_as_slab.shape, dtype=data_as_slab.dtype)
@@ -78,11 +83,12 @@ def apply_geometry_from_pixel_maps(data_as_slab, yx, im_out=None):
def pixel_maps_for_image_view(geometry_filename):
- """Parse the geometry file and pixel maps for an array in 'slab' format
- containing pixel values. The pixel maps can be used to create a representation
- of the physical layout of the detector in a pyqtgraph ImageView widget (i.e.
- they apply the detector geometry setting the origin of the reference
- system is in the top left corner of the output array).
+ """Parses a geometry file and creates pixel maps for pyqtgraph visualization.
+
+ Parse the geometry file and creates pixel maps for an array in 'slab' format containing pixel values. The pixel
+ maps can be used to create a representation of the physical layout of the detector in a pyqtgraph ImageView
+ widget (i.e. they apply the detector geometry setting the origin of the reference system is in the top left corner
+ of the output array).
Args:
@@ -92,12 +98,13 @@ def pixel_maps_for_image_view(geometry_filename):
(y, x) (numpy.ndarray int, numpy.ndarray int): pixel maps
- slab_shape tuple (int, int): shape of the original geometry uncorrected array
- (the pixel values in "slab" format).
+ slab_shape tuple (int, int): shape of the original geometry uncorrected array (the pixel values in "slab"
+ format).
- img_shape tuple (int, int): shape of the array needed to contain the
- representation of the physical layout of the detector.
+ img_shape tuple (int, int): shape of the array needed to contain the representation of the physical layout
+ of the detector.
"""
+
pixm = pixel_maps_from_geometry_file(geometry_filename)
x, y = pixm[0], pixm[1]
slab_shape = x.shape
@@ -117,8 +124,9 @@ def pixel_maps_for_image_view(geometry_filename):
def parse_xy(string):
- """Parse the x, y values from strings that have the format:
- '1x + 2.0y'.
+ """Extracts x and y values from strings in a geometry file.
+
+ Parse the x, y values from strings in that have the format: '1x + 2.0y'.
Args:
@@ -128,6 +136,7 @@ def parse_xy(string):
x, y (float, float): the values of x and y.
"""
+
x = y = 0
if string.find('x') is not -1:
@@ -147,9 +156,10 @@ def parse_xy(string):
def pixel_maps_from_geometry_file(fnam):
- """Extracts pixel maps from a CrystFEL-style geometry file. The pixel maps
- can be used to create a representation of the physical layout of the
- detector, keeping the origin of the reference system at the beam interaction
+ """Parses a geometry file and creates pixel maps.
+
+ Extracts pixel maps from a CrystFEL-style geometry file. The pixel maps can be used to create a representation of
+ the physical layout of the detector, keeping the origin of the reference system at the beam interaction
point.
Args:
@@ -158,9 +168,8 @@ def pixel_maps_from_geometry_file(fnam):
Returns:
- x,y,r (numpy.ndarray float, numpy.ndarray float, numpy.ndarray float):
- slab-like pixel maps with respectively x, y coordinates of the pixel
- and distance of the pixel from the center of the reference system
+ x,y,r (numpy.ndarray float, numpy.ndarray float, numpy.ndarray float): slab-like pixel maps with
+ respectively x, y coordinates of the pixel and distance of the pixel from the center of the reference system.
"""
f = open(fnam, 'r')
@@ -231,8 +240,9 @@ def pixel_maps_from_geometry_file(fnam):
def coffset_from_geometry_file(fnam):
- """Extracts detector distance offset information from a CrystFEL-style
- geometry file.
+ """Extracts detector distance information from a geometry file.
+
+ Extracts detector distance offset information from a CrystFEL-style geometry file.
Args:
@@ -242,6 +252,7 @@ def coffset_from_geometry_file(fnam):
coffset (float): the detector distance offset
"""
+
f = open(fnam, 'r')
f_lines = f.readlines()
f.close()
@@ -256,8 +267,9 @@ def coffset_from_geometry_file(fnam):
def res_from_geometry_file(fnam):
- """Extracts pixel resolution information from a CrystFEL-style
- geometry file.
+ """Extracts pixel resolution information from a geometry file.
+
+ Extracts pixel resolution information from a CrystFEL-style geometry file.
Args:
@@ -267,6 +279,7 @@ def res_from_geometry_file(fnam):
res (float): the pixel resolution
"""
+
f = open(fnam, 'r')
f_lines = f.readlines()
f.close()
diff --git a/cfelhdf5.py b/cfel_hdf5.py
similarity index 73%
rename from cfelhdf5.py
rename to cfel_hdf5.py
index 76946ae893549650b22a1cb95dd3640e30da1259..a789c314dc4746bbec49fbb0569ee8468520f655 100644
--- a/cfelhdf5.py
+++ b/cfel_hdf5.py
@@ -19,9 +19,13 @@ This module contains utilities for the processing of HDF5. This module builds
on what the h5py module already provides.
"""
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
-import numpy
import h5py
+import numpy
def load_nparray_from_hdf5_file(data_filename, data_group):
@@ -37,8 +41,11 @@ def load_nparray_from_hdf5_file(data_filename, data_group):
nparray (numpy.ndarray): numpy array with the data read from the file.
"""
-
- hdfile = h5py.File(data_filename, 'r')
- nparray = numpy.array(hdfile[data_group])
- hdfile.close()
- return nparray
+ try:
+ with h5py.File(data_filename, 'r') as hdfile:
+ nparray = numpy.array(hdfile[data_group])
+ hdfile.close()
+ except:
+ raise RuntimeError('Error reading file {0} (data block: {1}).'.format(data_filename, data_group))
+ else:
+ return nparray
diff --git a/cfeloptarg.py b/cfel_optarg.py
similarity index 81%
rename from cfeloptarg.py
rename to cfel_optarg.py
index e3746d3c50ca023759e9090f8cc9f92afd4b156b..40ec42061321e1b21f2b6390b3d7459a284d5a35 100644
--- a/cfeloptarg.py
+++ b/cfel_optarg.py
@@ -14,6 +14,12 @@
# along with cfelpyutils. If not, see <http://www.gnu.org/licenses/>.
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+
+
"""
Utilities for parsing command line options and configuration files.
@@ -22,30 +28,20 @@ configuration files.
"""
-import argparse
-import os
-
-
def parse_parameters(config):
"""Sets correct types for parameter dictionaries.
- Reads a parameter dictionary returned by the ConfigParser python modue,
- and assigns correct types to parameters, without changing the structure of
- the dictionary.
+ Reads a parameter dictionary returned by the ConfigParser python module, and assigns correct types to parameters,
+ without changing the structure of the dictionary.
- The parser tries to interpret each entry in the dictionary according to the
- following rules:
+ The parser tries to interpret each entry in the dictionary according to the following rules:
- - If the entry starts and ends with a single quote, it is interpreted as a
- string.
- - If the entry is the word None, without quotes, then the entry is
- interpreted as NoneType.
- - If the entry is the word False, without quotes, then the entry is
- interpreted as a boolean False.
- - If the entry is the word True, without quotes, then the entry is
- interpreted as a boolean True.
- - If non of the previous options match the content of the entry,
- the parser tries to interpret the entry in order as:
+ - If the entry starts and ends with a single quote, it is interpreted as a string.
+ - If the entry is the word None, without quotes, then the entry is interpreted as NoneType.
+ - If the entry is the word False, without quotes, then the entry is interpreted as a boolean False.
+ - If the entry is the word True, without quotes, then the entry is interpreted as a boolean True.
+ - If non of the previous options match the content of the entry, the parser tries to interpret the entry in order
+ as:
- An integer number.
- A float number.
@@ -59,8 +55,8 @@ def parse_parameters(config):
Returns:
- monitor_params (dict): dictionary with the same structure as the input
- dictionary, but with correct types assigned to each entry.
+ monitor_params (dict): dictionary with the same structure as the input dictionary, but with correct types
+ assigned to each entry.
"""
monitor_params = {}
@@ -84,11 +80,11 @@ def parse_parameters(config):
try:
monitor_params[sect][op] = int(monitor_params[sect][op])
continue
- except:
+ except ValueError:
try:
monitor_params[sect][op] = float(monitor_params[sect][op])
continue
- except:
+ except ValueError:
pass
return monitor_params
diff --git a/cfelpsana.py b/cfel_psana.py
similarity index 76%
rename from cfelpsana.py
rename to cfel_psana.py
index bdead5d49ecefdd5f3de2916d04aba176ca08b55..f17d8e9f73bfff48878b53effddb1020894b27d1 100644
--- a/cfelpsana.py
+++ b/cfel_psana.py
@@ -17,11 +17,16 @@
"""
Utilities based on the psana python module.
-This module provides utilities that build on the functionality provided by the
-psana python module.
+This module provides utilities that build on the functionality provided by the psana python module.
"""
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+
+
def psana_obj_from_string(name):
"""Converts a string into a psana object type.
@@ -46,9 +51,8 @@ def psana_obj_from_string(name):
def psana_event_inspection(source):
"""Prints the structure of psana events.
- Takes a psana source string (e.g. exp=CXI/cxix....) and inspects the
- structure of the first event in the data, printing information about
- the the content of the event.
+ Takes a psana source string (e.g. exp=CXI/cxix....) and inspects the structure of the first event in the data,
+ printing information about the the content of the event.
Args:
@@ -57,22 +61,8 @@ def psana_event_inspection(source):
import psana
- def my_import(name):
- mod = __import__(name)
- components = name.split('.')
- for comp in components[1:]:
- mod = getattr(mod, comp)
- return mod
-
- def my_psana_from_string(name):
- components = name.split('.')
- mod = __import__(components[0])
- for comp in components[1:]:
- mod = getattr(mod, comp)
- return mod
-
print('\n\n')
- print('data source : %s' % source)
+ print('data source :', source)
print('\n')
print('Opening dataset...')
@@ -91,8 +81,8 @@ def psana_event_inspection(source):
itr = ds.events()
evt = itr.next()
for k in evt.keys():
- print('Type: %s Source: %s Alias: %s Key: %s') % (k.type(), k.src(), k.alias(), k.key())
- print('\n')
+ print('Type: {0} Source: {1} Alias: {2} Key: {3}'.format(k.type(), k.src(), k.alias(), k.key()))
+ print('')
for k in evt.keys():
print(k)
@@ -104,9 +94,8 @@ def psana_event_inspection(source):
def dirname_from_source_runs(source):
"""Returns a directory name based on a psana source string.
- Takes a psana source string (e.g exp=CXI/cxix....) and returns
- a string that can be used as a subdirectory name or a prefix for files and
- directories.
+ Takes a psana source string (e.g exp=CXI/cxix....) and returns a string that can be used as a subdirectory name or
+ a prefix for files and directories.
Args:
@@ -125,5 +114,5 @@ def dirname_from_source_runs(source):
nums = runs.split(',')
if len(nums) == 0:
nums = runs
- dirname = 'run_' + "_".join(nums)
+ dirname = 'run_' + '_'.join(nums)
return dirname
diff --git a/cfelfabio.py b/cfelfabio.py
deleted file mode 100644
index ac7a46d951c2c851e216e443b28c378cc7197b6f..0000000000000000000000000000000000000000
--- a/cfelfabio.py
+++ /dev/null
@@ -1,57 +0,0 @@
-import numpy
-import fabio.cbfimage
-
-def read_cbf_from_stream(stream):
- """Reads a cbfimage object out of a data string buffer.
-
- Read a data string buffer received as a payload from the PETRAIII P11 sender,
- and creates a cbfimage object from it (See the documentation of the fabio
- python module).
-
- Args:
-
- stream (str): a data string buffer received from the PETRAIII P11 sender.
-
- Returns:
-
- cbf_obj (fabio.cbfimage): a cbfimage object containing the data extracted
- from the string buffer.
- """
-
- cbf_obj = fabio.cbfimage.cbfimage()
-
- cbf_obj.header = {}
- cbf_obj.resetvals()
-
- infile = stream
- cbf_obj._readheader(infile)
- if fabio.cbfimage.CIF_BINARY_BLOCK_KEY not in cbf_obj.cif:
- err = "Not key %s in CIF, no CBF image in stream" % (fabio.cbfimage.CIF_BINARY_BLOCK_KEY)
- logger.error(err)
- for kv in cbf_obj.cif.items():
- print("%s: %s" % kv)
- raise RuntimeError(err)
- if cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY] == "CIF Binary Section":
- cbf_obj.cbs += infile.read(len(fabio.cbfimage.STARTER) + int(cbf_obj.header["X-Binary-Size"]) - len(cbf_obj.cbs) + cbf_obj.start_binary)
- else:
- if len(cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY]) > int(cbf_obj.header["X-Binary-Size"]) + cbf_obj.start_binary + len(fabio.cbfimage.STARTER):
- cbf_obj.cbs = cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY][:int(cbf_obj.header["X-Binary-Size"]) + cbf_obj.start_binary + len(fabio.cbfimage.STARTER)]
- else:
- cbf_obj.cbs = cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY]
- binary_data = cbf_obj.cbs[cbf_obj.start_binary + len(fabio.cbfimage.STARTER):]
-
- if "Content-MD5" in cbf_obj.header:
- ref = numpy.string_(cbf_obj.header["Content-MD5"])
- obt = fabio.cbfimage.md5sum(binary_data)
- if ref != obt:
- logger.error("Checksum of binary data mismatch: expected %s, got %s" % (ref, obt))
-
- if cbf_obj.header["conversions"] == "x-CBF_BYTE_OFFSET":
- cbf_obj.data = cbf_obj._readbinary_byte_offset(binary_data).astype(cbf_obj.bytecode).reshape((cbf_obj.dim2, cbf_obj.dim1))
- else:
- raise Exception(IOError, "Compression scheme not yet supported, please contact the author")
-
- cbf_obj.resetvals()
- # ensure the PIL image is reset
- cbf_obj.pilimage = None
- return cbf_obj