small fixes and docs

docs/source/i07yaml.rst

@@ -0,0 +1,66 @@
+I07 YAML
+========
+
+A custom YAML input has been designed to enable the automated use of islatu at the I07 beamline.
+Here we document all of the options that are available in this interface.
+
+.. code-block:: yaml
+
+   # This is the beamline being used (optional, default 'i07')
+   instrument: 'i07'
+   visit:
+     # The instrument scientist name (optional, default 'My Local Contact')
+     local contact: 'A Local Contact'
+     # The name or names of the users (optional, default 'Unknown')
+     user: 'A User & Their Friend)'
+     # Where the user has come from (optional, default 'Unknown')
+     user affiliation: 'Some University'
+     # The visit id
+     visit id: 'siXXXXX-1'
+     # The current date (or starting date of the beamtime) (optional, default today)
+     date: 2020-XX-XX
+   crop:
+     # The cropping method to be used (either 'crop_peak' or 'crop')
+     # (optional, default 'crop_peak')
+     method: crop
+     # Kwargs as a dict (optional, default 'None')
+     # An example if 'crop' is used the pixel numbers are given
+     kwargs: {'x_start': 200, 'x_end':220, 'y_start': 70, 'y_end': 105}
+   background:
+     # How the background subtraction should be performed
+     # (either gaussian_1d or gaussian_2d)
+     # (optional, default gaussian_1d)
+     method: gaussian_1d
+     # The qxy axis of the detector image (optional, defaults 0)
+     axis: 0
+   setup:
+     # Full path to dcd normalisation file (required for dcd normalisation)
+     dcd normalisation: /dls/i07/data/2020/si24357-1/380396.dat
+     # Size of the sample if a tuple is passed these are taken as the value and uncertainty
+     sample size: (9e-3, 1e-3)
+     # Beam width at half maximum
+     beam width: 180e-6
+     # Name of the theta axis (optional, defaults 'dcdtheta')
+     theta axis: 'dcdtheta'
+     # Name of the q axis (optional, defaults 'qdcd')
+     q axis: qdcd
+     # If data should be transposes (rotated 90 degrees)
+     # (optional, defaults False)
+     transpose: False
+     # The maximum single pixel intensity (optional, defaults 1e6)
+     pixel max: 1e6
+     # The threshold for something to be investigated as a hot pixel
+     # (optional, 1e5)
+     hot pixel max: 1e5
+   # If rebin is not present the data will not be rebinned at all
+   rebin:
+     # Number of q vectors to be used (optional, default 50)
+     n qvectors: 50
+     # Alternatively a step size can be given (only used if n qvectors
+     # not given)
+     step: None
+     # A shape of binning can be set (either 'linear' or 'log')
+     # (optional, default 'log')
+     shape: log
+   # The number of columns to be output (optional, default 4)
+   output columns: 4

docs/source/index.rst

@@ -6,10 +6,10 @@
 X-ray reflectometry reduction in Python
 =======================================
 
-:py:mod:`islatu` is an open-source pacakge for the reduction of x-ray reflectometry datasets. 
-Currently, :py:mod:`islatu` is developed at and supports data from `Diamond Light Source`_, however we are happy to work with others to enable data from other sources (including neutron sources). 
+:py:mod:`islatu` is an open-source pacakge for the reduction of x-ray reflectometry datasets.
+Currently, :py:mod:`islatu` is developed at and supports data from `Diamond Light Source`_, however we are happy to work with others to enable data from other sources (including neutron sources).
 
-These webpages include `API-level documentation`_ and information about some `workflows`_ that can be used for data reduction. 
+These webpages include `API-level documentation`_ and information about some `workflows`_ that can be used for data reduction.
 
 Contributors
 ------------
@@ -32,6 +32,7 @@ We acknowledge the support of the Ada Lovelace Centre – a joint initiative bet
 
    installation
    workflows
+   i07yaml
    modules
 
 Searching

islatu/__init__.py

@@ -1,4 +1,4 @@
 MAJOR = 0
 MINOR = 0
-MICRO = 59
+MICRO = 60
 __version__ = '%d.%d.%d' % (MAJOR, MINOR, MICRO)

islatu/runner.py

@@ -32,12 +32,12 @@ def __init__(self, name='Unknown', affiliation='Unknown'):
 
 
 class Origin:
-    def __init__(self, contact=None, facility='Diamond Light Source', id=None,
+    def __init__(self, contact='My Local Contact', facility='Diamond Light Source', id=None,
                  title=None, directory_path=None):
         self.contact = contact
         self.facility = facility
         self.id = id
-        self.time = None
+        self.date = str(datetime.datetime.now())
         self.year = None
         self.title = title
         self.directory_path = directory_path
@@ -121,16 +121,14 @@ def __init__(self,
                  columns=['Qz / Aa^-1', 'RQz', 'sigma RQz, standard deviation',
                           'sigma Qz / Aa^-1, standard deviation'],
                  n_qvectors=50, q_min=None, q_max=None, q_step=None,
-                 q_shape='linear'):
+                 q_shape='log'):
         self.column_1 = columns[0]
         self.column_2 = columns[1]
         self.column_3 = columns[2]
         if len(columns) == 4:
             self.column_4 = columns[3]
         self.rebin = True
         self.n_qvectors = n_qvectors
-        self.q_min = q_min
-        self.q_max = q_max
         self.q_step = q_step
         self.q_shape = 'linear'
 
@@ -230,9 +228,9 @@ def setup(self, recipe):
             else:
                 raise ValueError("No beam width given in setup of {}.".format(
                     yaml_file))
-            if 'theta_axis' in recipe['setup'].keys():
+            if 'theta axis' in recipe['setup'].keys():
                 self.data_source.experiment.measurement.theta_axis_name = (
-                    recipe['setup']['theta_axis'])
+                    recipe['setup']['theta axis'])
             if 'q axis' in recipe['setup'].keys():
                 self.data_source.experiment.measurement.q_axis_name = (
                     recipe['setup']['q axis'])
@@ -242,12 +240,12 @@ def setup(self, recipe):
                 if self.data_source.experiment.measurement.transpose:
                     self.data_source.experiment.measurement.qz_dimension = 0
                     self.data_source.experiment.measurement.qxy_dimension = 1
-            if 'pixel_max' in recipe['setup'].keys():
+            if 'pixel max' in recipe['setup'].keys():
                 self.data_source.experiment.measurement.pixel_max = recipe[
-                    'setup']['pixel_max']
-            if 'hot_pixel_max' in recipe['setup'].keys():
+                    'setup']['pixel max']
+            if 'hot pixel max' in recipe['setup'].keys():
                 self.data_source.experiment.measurement.hot_pixel_max = recipe[
-                    'setup']['hot_pixel_max']
+                    'setup']['hot pixel max']
         else:
             raise ValueError("No setup given in {}.".format(yaml_file))
         if 'output_columns' in keys:
@@ -260,8 +258,6 @@ def setup(self, recipe):
                 self.data.n_qvectors = recipe['rebin']['n qvectors']
             elif 'min' in recipe['rebin'].keys() and 'max' in recipe[
                 'rebin'].keys() and 'step' in recipe['rebin'].keys():
-                self.data.q_min = recipe['rebin']['min']
-                self.data.q_max = recipe['rebin']['max']
                 self.data.q_step = recipe['rebin']['step']
                 if 'shape' in recipe['rebin'].keys():
                     self.data.q_shape = recipe['rebin']['shape']
@@ -272,7 +268,7 @@ def setup(self, recipe):
             self.data.rebin=False
 
 
-def reduce(run_numbers, yaml_file, directory='/dls/{}/data/{}/{}/',
+def i07reduce(run_numbers, yaml_file, directory='/dls/{}/data/{}/{}/',
            title='Unknown'):
     """
     The runner that parses the yaml file and performs the data reduction.
@@ -344,24 +340,25 @@ def reduce(run_numbers, yaml_file, directory='/dls/{}/data/{}/{}/',
                 spacing = np.linspace
             elif the_boss.data.q_space == 'log':
                 spacing = np.logspace
-            refl.rebin(new_q=spacing(the_boss.data.q_min, the_boss.data.q_max,
+            refl.rebin(new_q=spacing(refl.q.min(), refl.q.max(),
                                      the_boss.data.q_step))
         the_boss.reduction.data_state.rebinned = the_boss.data.q_shape
 
     the_boss.data_source.experiment.measurement.q_range = [
         str(refl.q.min()), str(refl.q.max())]
+    the_boss.data.n_qvectors = str(len(refl.R))
     try:
         _ = the_boss.data.column_4
         data = np.array([refl.q, refl.R, refl.dR, refl.dq]).T
         np.savetxt(
-            (the_boss.directory_path + '/processing/XRR_' +
-             run_numbers[0] + '.dat'), data,
+            (the_boss.directory_path + '/processing/XRR_{}.dat'.format(
+                run_numbers[0])), data,
              header='{}\n 1 2 3 4'.format(dump(vars(the_boss))))
     except:
         data = np.array([refl.q, refl.R, refl.dR]).T
         np.savetxt(
-            (the_boss.directory_path + '/processing/XRR_' +
-             run_numbers[0] + '.dat'), data,
+            (the_boss.directory_path + '/processing/XRR_{}.dat'.format(
+                run_numbers[0])), data,
              header='{}\n 1 2 3'.format(dump(vars(the_boss))))
 
     print("-" * 10)