From 223be18c3e451b8be2a962bba126f44c9eab41db Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 30 Mar 2022 17:40:06 +0200
Subject: [PATCH] Change default behaviour with 10+ plots

---
 beamtime/plotting.py | 20 ++++++++++++--------
 beamtime/xrd/io.py   |  6 ++----
 beamtime/xrd/plot.py | 13 ++++++++++---
 3 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/beamtime/plotting.py b/beamtime/plotting.py
index dd9a481..4e058ac 100644
--- a/beamtime/plotting.py
+++ b/beamtime/plotting.py
@@ -377,16 +377,20 @@ def update_rc_params(rc_params):
             plt.rcParams.update({key: rc_params[key]})
 
 
-def generate_colours(palettes):
+def generate_colours(palettes, kind=None):
 
-    # Creates a list of all the colours that is passed in the colour_cycles argument. Then makes cyclic iterables of these. 
-    colour_collection = []
-    for palette in palettes:
-        mod = importlib.import_module("palettable.colorbrewer.%s" % palette[0])
-        colour = getattr(mod, palette[1]).mpl_colors
-        colour_collection = colour_collection + colour
+    if kind == 'single':
+        colour_cycle = itertools.cycle(palettes)
 
-    colour_cycle = itertools.cycle(colour_collection)
+    else:
+        # Creates a list of all the colours that is passed in the colour_cycles argument. Then makes cyclic iterables of these. 
+        colour_collection = []
+        for palette in palettes:
+            mod = importlib.import_module("palettable.colorbrewer.%s" % palette[0])
+            colour = getattr(mod, palette[1]).mpl_colors
+            colour_collection = colour_collection + colour
+
+        colour_cycle = itertools.cycle(colour_collection)
 
 
     return colour_cycle
\ No newline at end of file
diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index 5aa2fb1..14c0f98 100644
--- a/beamtime/xrd/io.py
+++ b/beamtime/xrd/io.py
@@ -252,7 +252,7 @@ def read_brml(data, options={}, index=0):
 
                 start = float(chain.findall('ScanInformation/ScaleAxes/ScaleAxisInfo/Start')[0].text)
                 stop = float(chain.findall('ScanInformation/ScaleAxes/ScaleAxisInfo/Stop')[0].text)
-                increment = float(chain.findall('ScanInformation/ScaleAxes/ScaleAxisInfo/Increment')[0].text)
+                
 
 
 
@@ -262,7 +262,7 @@ def read_brml(data, options={}, index=0):
 
                         intensity = []
                         for r in raw:
-                            if r > 600:
+                            if r > 601:
                                 intensity.append(r)
 
                         intensity = np.array(intensity)
@@ -478,9 +478,7 @@ def translate_wavelengths(data, wavelength, to_wavelength=None):
 
 def find_wavelength_from_xy(path):
 
-    print(path)
 
- 
     wavelength_dict = {'Cu': 1.54059, 'Mo': 0.71073}
 
     with open(path, 'r') as f:
diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index 770b5a8..1a9429c 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -20,7 +20,7 @@ def plot_diffractogram(data, options={}):
 
     # Update options
     required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim', 'normalise', 'offset', 'offset_x', 'offset_y',
-    'reflections_plot', 'reflections_indices', 'reflections_data', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params']
+    'reflections_plot', 'reflections_indices', 'reflections_data', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params', 'interactive_session_active']
 
     default_options = {
         'x_vals': '2th', 
@@ -45,6 +45,10 @@ def plot_diffractogram(data, options={}):
         'format_params': {},
         }
 
+    if 'offset_y' not in options.keys():
+        if len(data['path']) > 10:
+            default_options['offset_y'] = 0.05
+
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
 
     # Convert data['path'] to list to allow iteration over this to accommodate both single and multiple diffractograms
@@ -62,6 +66,7 @@ def plot_diffractogram(data, options={}):
         for index in range(len(data['path'])):
             diffractogram, wavelength = xrd.io.read_data(data=data, options=options, index=index)
             
+            
             data['diffractogram'][index] = diffractogram
             data['wavelength'][index] = wavelength
 
@@ -113,7 +118,10 @@ def plot_diffractogram(data, options={}):
 
         ax = ax[-1]
 
-    colours = btp.generate_colours(options['palettes'])
+    if len(data['path']) < 10:
+        colours = btp.generate_colours(options['palettes'])
+    else:
+        colours = btp.generate_colours(['black'], kind='single')
 
 
     for diffractogram in data['diffractogram']:
@@ -183,7 +191,6 @@ def plot_diffractogram_interactive(data, options):
 
         if not ymax or (ymax < (diffractogram['I'].max())):#+index*options['offset_y'])):
             ymax = diffractogram['I'].max()#+index*options['offset_y']
-            print(ymax)
 
 
     ymin_start = ymin - 0.1*ymax