Bump version for bugfix release

eos/__init__.py

@@ -2,5 +2,5 @@
 Package to handle data redction at AMOR instrument to be used by __main__.py script.
 """
 
-__version__ = '3.0.4'
-__date__    = '2025-11-04'
+__version__ = '3.0.7'
+__date__    = '2025-12-01'

eos/event_analysis.py

@@ -25,8 +25,15 @@ class ExtractWalltime(EventDataAction):
         dataset.data.events = new_events
 
 class MergeFrames(EventDataAction):
+    def __init__(self, lamdaCut=None):
+        self.lamdaCut=lamdaCut
+
     def perform_action(self, dataset: EventDatasetProtocol)->None:
-        tofCut = const.lamdaCut*dataset.geometry.chopperDetectorDistance/const.hdm*1e-13
+        if self.lamdaCut is None:
+            lamdaCut = const.lamdaCut
+        else:
+            lamdaCut = self.lamdaCut
+        tofCut = lamdaCut*dataset.geometry.chopperDetectorDistance/const.hdm*1e-13
         total_offset = (tofCut +
                         dataset.timing.tau * (dataset.timing.ch1TriggerPhase + dataset.timing.chopperPhase/2)/180)
         dataset.data.events.tof = merge_frames(dataset.data.events.tof, tofCut, dataset.timing.tau, total_offset)

eos/file_reader.py

@@ -84,7 +84,7 @@ class AmorHeader:
         user_orcid = None
         sampleName = self.hdf['entry1/sample/name'][0].decode('utf-8')
         model = self.hdf['entry1/sample/model'][0].decode('utf-8')
-        if 'stack:' in model:
+        if 'stack' in model:
             import yaml
             model = yaml.safe_load(model)
         else:
@@ -223,7 +223,6 @@ class AmorEventData(AmorHeader):
 
     def __init__(self, fileName:Union[str, h5py.File, BinaryIO], first_index:int=0, max_events:int=100_000_000):
         if type(fileName) is str:
-            #logging.warning(f'    opening file {fileName}')
             logging.warning(f'    {fileName.split("/")[-1]}')
             self.file_list = [fileName]
             hdf = h5py.File(fileName, 'r', swmr=True)

eos/instrument.py

@@ -65,9 +65,14 @@ class LZGrid:
     def qzRange(self):
         return self._qzRange
 
-    def __init__(self, qResolution, qzRange):
+    def __init__(self, qResolution, qzRange, lambda_overwrite=None):
         self._qResolution = qResolution
         self._qzRange = qzRange
+        if lambda_overwrite is None:
+            self.lamdaMax = const.lamdaMax
+            self.lamdaCut = const.lamdaCut
+        else:
+            self.lamdaCut, self.lamdaMax = lambda_overwrite
 
     @property
     @cache
@@ -92,8 +97,8 @@ class LZGrid:
 
     @cache
     def lamda(self):
-        lamdaMax = 16
-        lamdaMin = const.lamdaCut
+        lamdaMax = self.lamdaMax
+        lamdaMin = self.lamdaCut
         lamda_grid = lamdaMin*(1+self.dldl)**np.arange(int(np.log(lamdaMax/lamdaMin)/np.log(1+self.dldl)+1))
         return lamda_grid
 

eos/projection.py

@@ -85,12 +85,19 @@ class ProjectedReflectivity:
         self.R -= R
         self.dR = np.sqrt(self.dR**2+dR**2)
 
+    def plot(self, **kwargs):
+        from matplotlib import pyplot as plt
+        plt.errorbar(self.Q, self.R, yerr=self.dR, **kwargs)
+        plt.yscale('log')
+        plt.xlabel('Q / Å$^{-1}$')
+        plt.ylabel('R')
 
 class LZProjection(ProjectionInterface):
     grid: LZGrid
     lamda: np.ndarray
     alphaF: np.ndarray
     is_normalized: bool
+    angle: float
 
     data: np.recarray
     _dtype = np.dtype([
@@ -107,6 +114,7 @@ class LZProjection(ProjectionInterface):
     def __init__(self, tthh: float, grid: LZGrid):
         self.grid = grid
         self.is_normalized = False
+        self.angle = tthh
 
         alphaF_z  = tthh + Detector.delta_z
         lamda_l  = self.grid.lamda()
@@ -206,12 +214,14 @@ class LZProjection(ProjectionInterface):
         Normalize the dataaset and take into account a difference in
         detector angle for measurement and reference.
         """
+        logging.debug(f'        correcting for incident angle difference from norm {norm.angle} to data {self.angle}')
         norm_lz = norm.norm
-        thetaN_z = Detector.delta_z+norm.angle
-        thetaN_lz = np.ones_like(norm_lz)*thetaN_z
-        thetaN_lz = np.where(np.absolute(thetaN_lz)>5e-3, thetaN_lz, np.nan)
-        self.data.mask &=  (np.absolute(thetaN_lz)>5e-3)
-        ref_lz = (self.data.I*np.absolute(thetaN_lz))/(norm_lz*np.absolute(self.alphaF))
+        delta_lz = np.ones_like(norm_lz)*Detector.delta_z
+        # do not perform gravity correction for footprint, would require norm detector distance that is unknown here
+        fp_corr_lz = np.where(np.absolute(delta_lz+norm.angle)>5e-3,
+                              (delta_lz+self.angle)/(delta_lz+norm.angle), np.nan)
+        self.data.mask &=  np.logical_not(np.isnan(fp_corr_lz))
+        ref_lz = self.data.I/norm_lz/fp_corr_lz
         ref_lz *= norm.monitor/self.monitor
         ref_lz[np.logical_not(self.data.mask)] = np.nan
         self.data.norm = norm_lz
@@ -298,7 +308,7 @@ class LZProjection(ProjectionInterface):
                 plt.colorbar(label='I / cpm')
         plt.xlabel('$\\lambda$ / $\\AA$')
         plt.ylabel('$\\Theta$ / °')
-        plt.xlim(3., 12.)
+        plt.xlim(self.lamda[0,0], self.lamda[-1,0])
         af = self.alphaF[self.data.mask]
         plt.ylim(af.min(), af.max())
         plt.title('Wavelength vs. Reflection Angle')

eos/reduction_e2h.py

@@ -51,6 +51,7 @@ class E2HReduction:
         self.plot_kwds = {}
         plt.rcParams.update({'font.size': self.config.reduction.fontsize})
 
+        self.overwrite = eh.ApplyParameterOverwrites(self.config.experiment) # some actions use instrument parameters, change before that
         if self.config.reduction.update:
             # live update implies plotting
             self.config.reduction.show_plot = True
@@ -68,6 +69,7 @@ class E2HReduction:
         # Actions on datasets not used for normalization
         self.event_actions = eh.ApplyPhaseOffset(self.config.experiment.chopperPhaseOffset)
         if not self.config.reduction.fast:
+            self.event_actions |= self.overwrite
             self.event_actions |= eh.CorrectChopperPhase()
             self.event_actions |= ea.ExtractWalltime()
         else:
@@ -88,7 +90,7 @@ class E2HReduction:
                 self.event_actions |= eh.TofTimeCorrection(self.config.experiment.incidentAngle==IncidentAngle.alphaF)
         # select needed actions in depenence of plots
         if self.config.reduction.plot in NEEDS_LAMDA or not self.config.experiment.is_default('lambdaRange'):
-            self.event_actions |= ea.MergeFrames()
+            self.event_actions |= ea.MergeFrames(lamdaCut=self.config.experiment.lambdaRange[0])
             self.event_actions |= ea.AnalyzePixelIDs(self.config.experiment.yRange)
             self.event_actions |= eh.TofTimeCorrection(self.config.experiment.incidentAngle==IncidentAngle.alphaF)
             self.event_actions |= ea.CalculateWavelength(self.config.experiment.lambdaRange)
@@ -96,8 +98,8 @@ class E2HReduction:
 
         # plot dependant options
         if self.config.reduction.plot in [E2HPlotSelection.All, E2HPlotSelection.LT, E2HPlotSelection.Q]:
-            self.grid = LZGrid(0.05, [0.0, 0.25])
-            self.grid.dldl = 0.05
+            self.grid = LZGrid(0.05, [0.0, 0.25], lambda_overwrite=self.config.experiment.lambdaRange)
+            self.grid.dldl = 0.01
 
         if self.config.reduction.plot in [E2HPlotSelection.All, E2HPlotSelection.Raw,
                                           E2HPlotSelection.LT, E2HPlotSelection.YT,
@@ -151,6 +153,7 @@ class E2HReduction:
 
     def prepare_graphs(self):
         last_file_header = AmorHeader(self.file_list[-1])
+        self.overwrite.perform_action(last_file_header)
         tthh  = last_file_header.geometry.nu - last_file_header.geometry.mu
 
         if not self.config.reduction.is_default('thetaRangeR'):

eos/reduction_reflectivity.py

@@ -117,7 +117,7 @@ class ReflectivityReduction:
             plt.show()
 
     def read_file_block(self, i, short_notation):
-        logging.warning('reading input:')
+        logging.warning('input:')
         file_list = self.path_resolver.resolve(short_notation)
 
         self.header.measurement_data_files = []
@@ -159,7 +159,7 @@ class ReflectivityReduction:
 
     def analyze_unsliced(self, i):
         self.monitor = self.dataset.data.pulses.monitor.sum()
-        logging.warning(f'    monitor = {self.monitor:8.2f} {MONITOR_UNITS[self.config.experiment.monitorType]}')
+        logging.info(f'    monitor = {self.monitor:8.2f} {MONITOR_UNITS[self.config.experiment.monitorType]}')
 
         proj:LZProjection = self.project_on_lz()
         try:

nicos_config.md

@@ -37,6 +37,7 @@ hist_tofz = device('nicos_sinq.devices.just_bin_it.JustBinItImage',
 ```
 
 These images have then to be set in the detector configuration as _images_ items:
+
 ```                      
 images=['hist_yz', 'hist_tofz'],
-```
+```