[io][utils] Adds function for writing comp info to h5 file

darfix/io/utils.py

@@ -26,9 +26,12 @@
 
 __authors__ = ["J. Garriga"]
 __license__ = "MIT"
-__date__ = "23/07/2019"
+__date__ = "06/02/2020"
 
 import logging
+import h5py
+from datetime import datetime
+import numpy
 
 _logger = logging.getLogger(__file__)
 
@@ -65,3 +68,90 @@ def advancement_display(iteration, total, prefix='', suffix='', decimals=1, leng
     # Print New Line on Complete
     if iteration == total:
         print()
+
+
+def write_process(h5_file, entry, dimensions, W, data, processing_order,
+                   data_path='/', overwrite=True):
+    """
+    Write a stack of components and its parameters into .h5
+
+    :param str h5_file: path to the hdf5 file
+    :param str entry: entry name
+    :param dict dimensions: Dictionary with the dimensions names and values
+    :param W: Matrix with the rocking curves values
+    :type: numpy.ndarray
+    :param data: Stack with the components
+    :type: numpy.ndarray
+    :param processing_order: processing order of treatment
+    :type: int
+    :param data_path: path to store the data
+    :type: str
+    """
+    process_name = 'process_' + str(processing_order)
+
+    def get_interpretation(my_data):
+        """Return hdf5 attribute for this type of data"""
+        if isinstance(my_data, numpy.ndarray):
+            if my_data.ndim is 1:
+                return 'spectrum'
+            elif my_data.ndim in (2, 3):
+                return 'image'
+        return None
+
+    def save_key(path_name, key_path, value):
+        """Save the given value to the associated path. Manage numpy arrays
+        and dictionaries"""
+        key_path = key_path.replace('.', '/')
+        # save if is dict
+        if isinstance(value, dict):
+            h5_path = '/'.join((path_name, key_path))
+            dicttoh5(value, h5file=h5_file, h5path=h5_path,
+                     overwrite_data=True, mode='a')
+        else:
+            with h5py.File(h5_file, 'a') as h5f:
+                nx = h5f.require_group(path_name)
+                try:
+                    nx[key_path] = value
+                except TypeError as e:
+                    _logger.error('Unable to write', str(key_path), 'reason is', str(e))
+                else:
+                    interpretation = get_interpretation(value)
+                    if interpretation:
+                        nx[key_path].attrs['interpretation'] = interpretation
+
+    with h5py.File(h5_file, 'a') as h5f:
+        h5f.attrs["default"] = "entry"
+        nx_entry = h5f.require_group('/'.join((data_path, entry)))
+        nx_entry.attrs["NX_class"] = "NXentry"
+        nx_entry.attrs["default"] = "data"
+
+        nx_process = nx_entry.require_group(process_name)
+        nx_process.attrs['NX_class'] = "NXprocess"
+        if overwrite:
+            for key in ('program', 'version', 'date', 'processing_order',
+                        'class_instance', 'ft'):
+                if key in nx_process:
+                    del nx_process[key]
+        nx_process['program'] = 'darfix'
+        nx_process['version'] = '0.2'
+        nx_process['date'] = datetime.now().replace(microsecond=0).isoformat()
+        nx_process['processing_order'] = numpy.int32(processing_order)
+
+        nx_parameters = nx_process.require_group("input")
+        nx_parameters.attrs['NX_class'] = "NXparameters"
+        nx_parameters_path = nx_parameters.name
+        results = nx_process.require_group("results")
+        results.attrs["NX_class"] = "NXcollection"
+        results_path = results.name
+
+        nx_data = nx_entry.require_group("data")
+        nx_data.attrs["NX_class"] = "NXdata"
+        nx_data.attrs["signal"] = "components"
+        source_addr = "entry/" + process_name + "/results/components"
+        results.attrs["target"] = "components"
+        save_key(results_path, "W", W)
+        save_key(results_path, "components", data)
+        nx_data["components"] = h5f[source_addr]
+
+    for key, value in dimensions.items():
+        save_key(nx_parameters_path, key_path=key, value=value)
\ No newline at end of file