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completed help and group entries for command line options

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This commit is contained in:
stahn
2025-09-05 14:39:46 +02:00
parent 03539eaea6
commit 03e2f461cb
2 changed files with 51 additions and 35 deletions
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83
libeos/options.py
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@@ -178,15 +178,15 @@ class ReaderConfig(ArgParsable):
metadata={
'short': 'rp',
'group': 'input data',
'help': 'Search paths for hdf files',
'help': 'search paths for hdf files',
},
)
startTime: Optional[float] = field(
default = None,
metadata={
'short': '?',
'group': '?',
'help': '?',
'short': 'st',
'group': 'data manicure',
'help': 'set time zero other than the start of the data aquisition',
},
)
@@ -204,7 +204,6 @@ class MonitorType(StrEnum):
@dataclass
class ExperimentConfig(ArgParsable):
#chopperPhase: float
chopperPhase: float = field(
default=0,
metadata={
@@ -221,7 +220,6 @@ class ExperimentConfig(ArgParsable):
'help': 'phase between chopper 1 index pulse and closing edge',
},
)
#chopperSpeed: float
chopperSpeed: float = field(
default=500,
metadata={
@@ -230,26 +228,22 @@ class ExperimentConfig(ArgParsable):
'help': 'rotation speed of the chopper disks in rpm',
},
)
#yRange: Tuple[float, float]
yRange: Tuple[float, float] = field(
default_factory=lambda: [18, 48],
#default=[18, 48],
metadata={
'short': 'y',
'group': 'instrument settings',
'group': 'region of interest',
'help': 'horizontal pixel range on the detector to be used',
},
)
#lambdaRange: Tuple[float, float]
lambdaRange: Tuple[float, float] = field(
default_factory=lambda: [3, 12.5],
metadata={
'short': 'l',
'group': 'instrument settings',
'group': 'region of interest',
'help': 'wavelength range to be used (in angstrom)',
},
)
#lowCurrentThreshold: float
lowCurrentThreshold: float = field(
default=50,
metadata={
@@ -259,13 +253,22 @@ class ExperimentConfig(ArgParsable):
},
)
incidentAngle: IncidentAngle = IncidentAngle.alphaF
#sampleModel: Optional[str] = None
incidentAngle: str = field(
default=IncidentAngle.alphaF,
metadata={
'short': 'ai',
'group': 'instrument settings',
'help': 'calculate alphaI = [alphaF], [mu]+kappa+delta_kappa or ([nu]+kappa+delta_kappa)/2',
},
)
alphaF = 'alphaF'
mu = 'mu'
nu = 'nu'
sampleModel: Optional[str] = field(
default=None,
metadata={
'short': 'sm',
'group': '?',
'group': 'sample',
'help': 'orso type string to describe the sample in one line',
},
)
@@ -273,7 +276,7 @@ class ExperimentConfig(ArgParsable):
default=None,
metadata={
'short': 'mu',
'group': '?',
'group': 'sample',
'help': 'inclination of the sample surface w.r.t. the instrument horizon',
},
)
@@ -281,7 +284,7 @@ class ExperimentConfig(ArgParsable):
default=None,
metadata={
'short': 'nu',
'group': '?',
'group': 'sample',
'help': 'inclination of the detector w.r.t. the instrument horizon',
},
)
@@ -289,7 +292,7 @@ class ExperimentConfig(ArgParsable):
default=0,
metadata={
'short': 'm',
'group': '?',
'group': 'sample',
'help': 'correction offset for mu misalignment (mu_real = mu_file + mu_offset)',
},
)
@@ -313,15 +316,15 @@ class ReductionConfig(ArgParsable):
default=0.01,
metadata={
'short': 'r',
'group': '?',
'help': '?',
'group': 'data manicure',
'help': 'output resolution of q-scale Delta q / q',
},
)
qzRange: Tuple[float, float] = field(
default_factory=lambda: [0.005, 0.51],
metadata={
'short': 'q',
'group': '?',
'group': 'region of interest',
'help': '?',
},
)
@@ -329,8 +332,8 @@ class ReductionConfig(ArgParsable):
default_factory=lambda: [-12., 12.],
metadata={
'short': 't',
'group': '?',
'help': '?',
'group': 'region of interest',
'help': 'absolute theta region of interest',
},
)
#thetaRangeR: Tuple[float, float]
@@ -338,8 +341,8 @@ class ReductionConfig(ArgParsable):
default_factory=lambda: [-0.75, 0.75],
metadata={
'short': 'T',
'group': '?',
'help': '?',
'group': 'region of interest',
'help': 'theta region of interest w.r.t. beam center',
},
)
fileIdentifier: List[str] = field(
@@ -360,10 +363,22 @@ class ReductionConfig(ArgParsable):
'group': 'input data',
'help': 'normalisation method: [o]verillumination, [u]nderillumination, [d]irect_beam'})
scale: List[float] = field(
default_factory=lambda: [1.]
) #per file scaling; if less elements than files use the last one
autoscale: bool = False # TODO: This made no sense, it is used as single bool.
default_factory=lambda: [1.],
metadata={
'short': 's',
'group': 'data manicure',
'help': '(list of) scaling factors, if less elements than files use the last one',
},
)
# TODO: This made no sense, it is used as single bool.
autoscale: Tuple[float, float] = field(
default_factory=lambda: [None, None],
metadata={
'short': 'S',
'group': 'data manicure',
'help': '',
},
)
subtract: Optional[str] = field(
default=None,
metadata={
@@ -381,7 +396,7 @@ class ReductionConfig(ArgParsable):
default_factory=lambda: [None],
metadata={
'short': 'ts',
'group': '?',
'group': 'region of interest',
'help': 'time slizing <interval> ,[<start> [,stop]]',
},
)
@@ -392,15 +407,15 @@ class OutputConfig(ArgParsable):
default_factory=lambda: ['Rqz.ort'],
metadata={
'short': 'of',
'group': '?',
'help': '?',
'group': 'output',
'help': 'one of "Rqz[.ort]", "Rlt[.ort]" or both with "ort"',
},
)
outputName: str = field(
default='fromEOS',
metadata={
'short': 'o',
'group': '?',
'group': 'output',
'help': '?',
},
)
@@ -408,7 +423,7 @@ class OutputConfig(ArgParsable):
default='.',
metadata={
'short': 'op',
'group': '?',
'group': 'output',
'help': '?',
},
)

3
libeos/reduction.py
View File

@@ -465,7 +465,8 @@ class AmorReduction:
if self.monitor > 1e-6 :
ref_lz *= self.normMonitor / self.monitor
else:
logging.info(' low monitor -> zero output')
logging.info(' low monitor -> nan output')
ref_lz *= np.nan
err_lz = ref_lz * np.sqrt( 1/(int_lz+.1) + 1/norm_lz )
# TODO: allow for non-ideal Delta lambda / lambda (rather than 2.2%)