From ebb98debffb2a4166e3aed5f3bbecbd126ccfe98 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Tue, 15 Mar 2022 17:13:17 +0100
Subject: [PATCH] Open beamline data straight from raw file

---
 beamtime/xrd/io.py   | 49 ++++++++++++++++++++++++--------------------
 beamtime/xrd/plot.py |  6 ++----
 2 files changed, 29 insertions(+), 26 deletions(-)

diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index 347eed1..43ae2f7 100644
--- a/beamtime/xrd/io.py
+++ b/beamtime/xrd/io.py
@@ -23,15 +23,14 @@ def get_image_headers(path):
     return image.header
 
 
-def integrate_1d(calibrant, bins, path=None, image=None, options=None):
+def integrate_1d(data, options={}):
     ''' Integrates an image file to a 1D diffractogram. 
 
-    Input:
-    calibrant: path to .poni-file
-    bins: Number of bins to divide image into
-    path (optional): path to image file - either this or image must be specified. If both is passed, image is prioritsed
-    image (optional): image array (Numpy) as extracted from get_image_array
-    options (optional): dictionary of options
+    Required content of data:
+    calibrant (str): path to .poni-file
+    nbins (int): Number of bins to divide image into
+    path (str) (optional): path to image file - either this or image must be specified. If both is passed, image is prioritsed
+    image (str) (optional): image array (Numpy) as extracted from get_image_array
 
     Output:
     df: DataFrame contianing 1D diffractogram if option 'return' is True
@@ -56,15 +55,15 @@ def integrate_1d(calibrant, bins, path=None, image=None, options=None):
                 options[option] = default_options[option]
     
     
-    if not image:
-        image = get_image_array(path)
+    if 'image' not in data.keys():
+        data['image'] = get_image_array(data['path'])
     
-    ai = pyFAI.load(calibrant)
+    ai = pyFAI.load(data['calibrant'])
 
 
     if not options['filename']:
-        if path:
-            filename = os.path.join(options['save_folder'], os.path.split(path)[-1].split('.')[0] + options['extension'])
+        if data['path']:
+            filename = os.path.join(options['save_folder'], os.path.split(data['path'])[-1].split('.')[0] + options['extension'])
         else:
             filename = os.path.join(options['save_folder'], 'integrated.dat')
 
@@ -84,10 +83,9 @@ def integrate_1d(calibrant, bins, path=None, image=None, options=None):
         os.makedirs(options['save_folder'])
 
 
-    res = ai.integrate1d(image, bins, unit=options['unit'], filename=filename)
+    res = ai.integrate1d(data['image'], data['nbins'], unit=options['unit'], filename=filename)
 
-    if options['return']:
-        return read_diffractogram(filename)
+    return read_diffractogram(filename)
     
 
 
@@ -245,16 +243,23 @@ def read_diffractogram(path):
     return diffractogram
 
 
-def read_data(path, kind, options=None):
+def read_data(data, options={}):
 
-    if kind == 'beamline':
-        diffractogram = read_diffractogram(path)
+    if data['plot_kind'] == 'beamline':
 
-    elif kind == 'recx':
-        diffractogram = read_brml(path, options=options)
+        beamline = ['mar3450', 'edf', 'cbf']
 
-    elif kind == 'image':
-        diffractogram = get_image_array(path)
+        if data['path'].split('.')[-1] in beamline:
+            diffractogram = integrate_1d(data=data, options=options)
+        
+        else:
+            diffractogram = read_diffractogram(data['path'])
+
+    elif data['plot_kind'] == 'recx':
+        diffractogram = read_brml(data['path'], options=options)
+
+    elif data['plot_kind'] == 'image':
+        diffractogram = get_image_array(data['path'])
 
 
     return diffractogram
diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index c9ecc77..25a91cf 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -19,7 +19,7 @@ def plot_diffractogram(plot_data, options={}):
     plot_data (dict): Must include path = string to diffractogram data, and plot_kind = (recx, beamline, image)'''
 
     # Update options
-    required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 
+    required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim',
     'reflections_plot', 'reflections_indices', 'reflections_data', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params']
 
     default_options = {
@@ -59,8 +59,6 @@ def plot_diffractogram(plot_data, options={}):
     if len(options['reflections_data']) >= 1:
         options = determine_grid_layout(options=options)
 
-        print(options['format_params']['nrows'])
-
 
     # Prepare plot, and read and process data
 
@@ -84,7 +82,7 @@ def plot_diffractogram(plot_data, options={}):
     colours = btp.generate_colours(options['palettes'])
 
 
-    diffractogram = xrd.io.read_data(path=plot_data['path'], kind=plot_data['plot_kind'], options=options)
+    diffractogram = xrd.io.read_data(data=plot_data)
 
 
     if options['line']: