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__ = '3.0.5'
-__date__    = '2025-11-04'
+__version__ = '3.0.7'
+__date__    = '2025-12-01'

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/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

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:
@@ -97,7 +99,7 @@ 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], lambda_overwrite=self.config.experiment.lambdaRange)
-            self.grid.dldl = 0.05
+            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'],
-```
+```