Move execution script from eos.py to package and rename package to eos, add entry point to setup

.gitignore

@@ -8,3 +8,5 @@ raw
 test_results
 build
 dist
+profile_test.prof
+amor_eos.log

eos.py

@@ -1,48 +0,0 @@
-#!/usr/bin/env python
-"""
-eos reduces measurements performed on Amor@SINQ, PSI
-
-Author: Jochen Stahn (algorithms, python draft),
-        Artur Glavic (structuring and optimisation of code)
-
-conventions (not strictly followed, yet):
-- array names end with the suffix '_x[y]' with the meaning
-    _e  = events
-    _tof
-    _l  = lambda
-    _t  = theta
-    _z  = detector z
-    _lz = (lambda, detector z)
-    _q  = q_z
-"""
-
-import logging
-
-from libeos.command_line import command_line_options
-from libeos.logconfig import setup_logging
-
-#=====================================================================================================
-# TODO:
-# - calculate resolution using the chopperPhase
-# - deal with background correction
-# - format of 'call' + add '-Y' if not supplied
-#=====================================================================================================
-
-def main():
-    setup_logging()
-    logging.warning('######## eos - data reduction for Amor ########')
-
-    # read command line arguments and generate classes holding configuration parameters
-    config = command_line_options()
-
-    # only import heavy module if sufficient command line parameters were provieded
-    from libeos.reduction import AmorReduction
-    # Create reducer with these arguments
-    reducer = AmorReduction(config)
-    # Perform actual reduction
-    reducer.reduce()
-
-    logging.info('######## eos - finished ########')
-
-if __name__ == '__main__':
-    main()

eos/__init__.py

@@ -1,5 +1,5 @@
 """
-Package to handle data redction at AMOR instrument to be used by eos.py script.
+Package to handle data redction at AMOR instrument to be used by __main__.py script.
 """
 
 __version__ = '3.0.0'

eos/__main__.py

@@ -0,0 +1,41 @@
+"""
+eos reduces measurements performed on Amor@SINQ, PSI
+
+Author: Jochen Stahn (algorithms, python draft),
+        Artur Glavic (structuring and optimisation of code)
+"""
+
+import logging
+
+# need to do absolute import here as pyinstaller requires it
+from eos.options import EOSConfig, ReaderConfig, ExperimentConfig, ReductionConfig, OutputConfig
+from eos.command_line import commandLineArgs
+from eos.logconfig import setup_logging, update_loglevel
+
+def main():
+    setup_logging()
+
+    # read command line arguments and generate classes holding configuration parameters
+    clas = commandLineArgs([ReaderConfig, ExperimentConfig, ReductionConfig, OutputConfig],
+                           'eos')
+    update_loglevel(clas.verbose)
+
+    reader_config = ReaderConfig.from_args(clas)
+    experiment_config = ExperimentConfig.from_args(clas)
+    reduction_config = ReductionConfig.from_args(clas)
+    output_config = OutputConfig.from_args(clas)
+    config = EOSConfig(reader_config, experiment_config, reduction_config, output_config)
+
+    logging.warning('######## eos - data reduction for Amor ########')
+
+    # only import heavy module if sufficient command line parameters were provided
+    from eos.reduction import AmorReduction
+    # Create reducer with these arguments
+    reducer = AmorReduction(config)
+    # Perform actual reduction
+    reducer.reduce()
+
+    logging.info('######## eos - finished ########')
+
+if __name__ == '__main__':
+    main()

eos/command_line.py

@@ -1,10 +1,10 @@
 import argparse
 
-from .logconfig import update_loglevel
-from .options import ReaderConfig, EOSConfig, ExperimentConfig, OutputConfig, ReductionConfig
+from typing import List
+from .options import ArgParsable
 
 
-def commandLineArgs():
+def commandLineArgs(config_items: List[ArgParsable], program_name=None):
     """
     Process command line argument.
     The type of the default values is used for conversion and validation.
@@ -12,14 +12,15 @@ def commandLineArgs():
     msg = "eos reads data from (one or several) raw file(s) of the .hdf format, \
            performs various corrections, conversations and projections and exports\
            the resulting reflectivity in an orso-compatible format."
-    clas = argparse.ArgumentParser(description = msg, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    clas = argparse.ArgumentParser(prog=program_name,
+                                   description = msg, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
     clas.add_argument('-v', '--verbose', action='count', default=0)
 
     clas_groups = {}
 
     all_arguments = []
-    for cls in [ReaderConfig, ExperimentConfig, OutputConfig, ReductionConfig]:
+    for cls in config_items:
         all_arguments += cls.get_commandline_parameters()
 
     all_arguments.sort() # parameters are sorted alphabetically, unless they have higher priority
@@ -36,16 +37,3 @@ def commandLineArgs():
                     )
 
     return clas.parse_args()
-
-
-
-def command_line_options():
-    clas   = commandLineArgs()
-    update_loglevel(clas.verbose)
-
-    reader_config = ReaderConfig.from_args(clas)
-    experiment_config = ExperimentConfig.from_args(clas)
-    reduction_config = ReductionConfig.from_args(clas)
-    output_config = OutputConfig.from_args(clas)
-
-    return EOSConfig(reader_config, experiment_config, reduction_config, output_config)

eos/helpers_fallback.py

@@ -18,8 +18,8 @@ def extract_walltime(tof_e, dataPacket_p, dataPacketTime_p):
 def filter_project_x(pixelLookUp, pixelID_e, ymin, ymax):
     (detY_e, detZ_e, detXdist_e, delta_e) = pixelLookUp[np.int_(pixelID_e)-1, :].T
     # define mask and filter y range
-    mask_e = (ymin<=detY_e) & (detY_e<=ymax[1])
-    return (detY_e, detZ_e, detXdist_e, delta_e, mask_e)
+    mask_e = (ymin<=detY_e) & (detY_e<=ymax)
+    return (detZ_e, detXdist_e, delta_e, mask_e)
 
 def calculate_derived_properties_focussing(tof_e, detXdist_e, delta_e, mask_e,
                                            lmin, lmax, nu, mu, chopperDetectorDistance, hdm):

eos/options.py

@@ -297,6 +297,15 @@ class NormalisationMethod(StrEnum):
 
 @dataclass
 class ReductionConfig(ArgParsable):
+    fileIdentifier: List[str] = field(
+            metadata={
+                'short':    'f',
+                'priority': 100,
+                'group':    'input data',
+                'help':     'file number(s) or offset (if < 1)',
+                },
+            )
+
     qResolution: float = field(
             default=0.01,
             metadata={
@@ -329,15 +338,6 @@ class ReductionConfig(ArgParsable):
                 'help': 'theta region of interest w.r.t. beam center',
                 },
             )
-    fileIdentifier: List[str] = field(
-            default_factory=lambda: ['0'],
-            metadata={
-                'short': 'f', 
-                'priority': 100,
-                'group': 'input data', 
-                'help': 'file number(s) or offset (if < 1)',
-                },
-            )
     normalisationMethod: NormalisationMethod = field(
             default=NormalisationMethod.over_illuminated,
             metadata={
@@ -492,7 +492,7 @@ class EOSConfig:
     #        return self.calculate_call_string()
     
     def call_string(self):
-        base = 'python eos.py'
+        base = 'eos'
         
         inpt = ''
         if self.reader.year:

setup.cfg

@@ -3,7 +3,7 @@ universal = 1
 
 [metadata]
 name = amor_eos
-version = attr: libeos.__version__
+version = attr: eos.__version__
 author = Jochen Stahn - Paul Scherrer Institut
 author_email = jochen.stahn@psi.ch
 description = EOS reflectometry reduction for AMOR instrument
@@ -19,9 +19,7 @@ classifiers =
 [options]
 python_requires = >=3.8
 packages =
-    libeos
-scripts =
-    eos.py
+    eos
 install_requires =
     numpy
     h5py
@@ -30,3 +28,7 @@ install_requires =
 
 [project.urls]
 Homepage = "https://github.com/jochenstahn/amor"
+
+[options.entry_points]
+console_scripts =
+    eos = eos.__main__:main

tests/test_full_analysis.py

@@ -2,7 +2,7 @@ import os
 import cProfile
 from unittest import TestCase
 from dataclasses import fields, MISSING
-from libeos import options, reduction, logconfig
+from eos import options, reduction, logconfig
 
 logconfig.setup_logging()
 logconfig.update_loglevel(1)

windows_build.spec

@@ -2,7 +2,7 @@
 
 
 a = Analysis(
-    ['eos.py'],
+    ['eos/__main__.py'],
     pathex=[],
     binaries=[],
     datas=[],

windows_folder.spec

@@ -9,7 +9,7 @@ datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
 
 
 a = Analysis(
-    ['eos.py'],
+    ['eos/__main__.py'],
     pathex=[],
     binaries=[],
     datas=[],