From 903c1a3f51cf9c4a533fecf6b7542e85aabea692 Mon Sep 17 00:00:00 2001
From: Philip Mousley <philipmousley@hotmail.com>
Date: Fri, 10 Jan 2025 10:06:48 +0000
Subject: [PATCH] add in option to save unnormalised intensity

---
 src/islatu/data.py   | 13 +++++++++++++
 src/islatu/runner.py | 11 +++++++++--
 2 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/src/islatu/data.py b/src/islatu/data.py
index 7397c0d..267667d 100644
--- a/src/islatu/data.py
+++ b/src/islatu/data.py
@@ -81,6 +81,19 @@ def reflectivity_e(self) -> np.array:
         intensity array.
         """
         return self.intensity_e/np.amax(self.intensity)
+    @property
+    def reflectivity_nonorm(self) -> np.array:
+        """
+        Returns the intensity, unnormalised
+        """
+        return self.intensity
+
+    @property
+    def reflectivity_e_nonorm(self) -> np.array:
+        """
+        Returns the errors on the intensity, unnormalised
+        """
+        return self.intensity_e
 
     @property
     def q_vectors(self) -> np.array:
diff --git a/src/islatu/runner.py b/src/islatu/runner.py
index 0a95399..62355ed 100644
--- a/src/islatu/runner.py
+++ b/src/islatu/runner.py
@@ -140,7 +140,7 @@ def __init__(self, software=Software(), input_files=None,
                  data_state=DataState(), parser=io.i07_nxs_parser,
                  crop_function=cropping.crop_to_region, crop_kwargs=None,
                  bkg_function=background.fit_gaussian_1d, bkg_kwargs=None,
-                 dcd_normalisation=None, sample_size=None, beam_width=None,overwrite_transmission=None):
+                 dcd_normalisation=None, sample_size=None, beam_width=None,overwrite_transmission=None,normalisation=True):
         if input_files is None:
             input_files = []
         self.software = software
@@ -155,6 +155,7 @@ def __init__(self, software=Software(), input_files=None,
         self.sample_size = sample_size
         self.beam_width = beam_width
         self.overwrite_transmission=overwrite_transmission
+        self.normalisation=normalisation
 
 
 class Data:
@@ -258,6 +259,9 @@ def setup(self, recipe):
                 self.reduction.bkg_kwargs = recipe['background']['kwargs']
         if 'transmission' in keys:
             self.reduction.overwrite_transmission=recipe['transmission']['values']
+            
+        if 'normalisation' in keys:
+            self.reduction.normalisation=recipe['normalisation']['maxnorm']
         # Populate the setup information
         if 'setup' in keys:
             if 'dcd normalisation' in recipe['setup'].keys():
@@ -493,7 +497,10 @@ def i07reduce(run_numbers, yaml_file, directory='/dls/{}/data/{}/{}/',
 
 
     # Prepare the data array.
-    data = np.array([refl.q_vectors, refl.reflectivity, refl.reflectivity_e]).T
+    if the_boss.reduction.normalisation==True:
+        data = np.array([refl.q_vectors, refl.reflectivity, refl.reflectivity_e]).T
+    elif the_boss.reduction.normalisation==False:
+        data = np.array([refl.q_vectors, refl.reflectivity_nonorm, refl.reflectivity_e_nonorm]).T
     debug.log("XRR reduction completed.", unimportance=2)
 
     # Work out where to save the file.