From e651b64b9cc2d823041fa1463a666b1e9eeaff9d Mon Sep 17 00:00:00 2001
From: jochenstahn <jochen.stahn@psi.ch>
Date: Wed, 11 Sep 2024 18:22:39 +0200
Subject: [PATCH] introduced underillumination option

---
 libeos/command_line.py |  8 ++++----
 libeos/options.py      |  4 ++--
 libeos/reduction.py    | 14 +++++++++++++-
 3 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/libeos/command_line.py b/libeos/command_line.py
index d92f788..22152f7 100644
--- a/libeos/command_line.py
+++ b/libeos/command_line.py
@@ -24,9 +24,9 @@ def commandLineArgs():
                             default = Defaults.normalisationFileIdentifier,
                             nargs = '+',
                             help = "file number(s) of normalisation measurement")
-    #input_data.add_argument("-nm", "--normalisationMethod",
-    #                        default = Defaults.normalisationMethod,
-    #                        help = "normalisation method: overillumination, underillumination, direct_beam")
+    input_data.add_argument("-nm", "--normalisationMethod",
+                            default = Defaults.normalisationMethod,
+                            help = "normalisation method: [o]verillumination, [u]nderillumination, [d]irect_beam")
     input_data.add_argument("--raw", 
                             type = str,
                             default = Defaults.raw,
@@ -198,7 +198,7 @@ def command_line_options():
         scale                        = clas.scale,
         subtract                     = clas.subtract,
         normalisationFileIdentifier  = clas.normalisationFileIdentifier,
-        #normalisationMethod          = clas.normalisationMethod,
+        normalisationMethod          = clas.normalisationMethod,
         timeSlize                    = clas.timeSlize,
         )
     output_config = OutputConfig(
diff --git a/libeos/options.py b/libeos/options.py
index daf9a67..943fec8 100644
--- a/libeos/options.py
+++ b/libeos/options.py
@@ -12,7 +12,7 @@ class Defaults:
     raw                         = ['.', './raw', '../raw', '../../raw']
     year                        = datetime.now().year
     normalisationFileIdentifier = []
-    #normalisationMethod         = 'overillumination'
+    normalisationMethod         = 'o'
     # subtract
     outputName                  = "fromEOS"
     outputFormat                = ['Rqz.ort']
@@ -60,6 +60,7 @@ class ExperimentConfig:
 
 @dataclass
 class ReductionConfig:
+    normalisationMethod: str
     qResolution: float
     qzRange: Tuple[float, float]
     thetaRange: Tuple[float, float]
@@ -71,7 +72,6 @@ class ReductionConfig:
     autoscale: Optional[Tuple[bool, bool]] = None
     subtract: Optional[str] = None
     normalisationFileIdentifier: Optional[list] = None
-    #normalisationMethod: str
     timeSlize: Optional[list] = None
 
 @dataclass
diff --git a/libeos/reduction.py b/libeos/reduction.py
index dee7ddb..6025b78 100644
--- a/libeos/reduction.py
+++ b/libeos/reduction.py
@@ -408,7 +408,19 @@ class AmorReduction:
         int_lz    = np.where(mask_lz, int_lz, np.nan)
         thetaF_lz = np.where(mask_lz, alphaF_lz, np.nan)
 
-        ref_lz    = (int_lz * np.absolute(thetaN_lz)) / (norm_lz * np.absolute(thetaF_lz)) * self.normMonitor
+        print(self.reduction_config.normalisationMethod)
+        if self.reduction_config.normalisationMethod == 'o':
+            logging.debug('      assuming an overilluminated sample and correcting for the angle of incidence')
+            ref_lz    = (int_lz * np.absolute(thetaN_lz)) / (norm_lz * np.absolute(thetaF_lz)) * self.normMonitor
+        elif self.reduction_config.normalisationMethod == 'u':
+            logging.debug('      assuming an underilluminated sample and ignoring the angle of incidence')
+            ref_lz    = (int_lz / norm_lz) * self.normMonitor
+        elif self.reduction_config.normalisationMethod == 'u':
+            logging.debug('      assuming direct beam for normalisation an underilluminated sample and ignoring the angle of incidence')
+            ref_lz    = (int_lz / norm_lz) * self.normMonitor
+        else:
+            logging.debug('unknown normalisation method! Use [u], [o] or [d]')
+            ref_lz    = (int_lz * np.absolute(thetaN_lz)) / (norm_lz * np.absolute(thetaF_lz)) * self.normMonitor
         err_lz    = ref_lz * np.sqrt( 1/(int_lz+.1) + 1/norm_lz ) 
 
         res_lz    = np.ones((np.shape(lamda_l[:-1])[0], np.shape(alphaF_z)[0])) * 0.022**2