work on the fit widget

kmap/gui/process/FitWidget.py

@@ -182,20 +182,23 @@ class FitWidget(Qt.QDialog):
                            fit_type=self.__fitType,
                            roiIndices=self.__roiIndices)
         with FitH5Writer(self.__selectedFile, mode='w') as fitH5:
-            fitH5.set_x_fit(results.x_height,
-                            results.x_center,
-                            results.x_width)
-            fitH5.set_y_fit(results.y_height,
-                            results.y_center,
-                            results.y_width)
-            fitH5.set_z_fit(results.z_height,
-                            results.z_center,
-                            results.z_width)
-            fitH5.set_scan_positions(results.sample_x, results.sample_y)
-            fitH5.set_status(results.status)
-            fitH5.set_x_axis(results.q_x)
-            fitH5.set_y_axis(results.q_y)
-            fitH5.set_z_axis(results.q_z)
+            fitH5.create_entry(results.fit_name)
+            fitH5.create_process(results.fit_name)
+            fitH5.
+            # fitH5.set_x_fit(results.x_height,
+            #                 results.x_center,
+            #                 results.x_width)
+            # fitH5.set_y_fit(results.y_height,
+            #                 results.y_center,
+            #                 results.y_width)
+            # fitH5.set_z_fit(results.z_height,
+            #                 results.z_center,
+            #                 results.z_width)
+            # fitH5.set_scan_positions(results.sample_x, results.sample_y)
+            # fitH5.set_status(results.status)
+            # fitH5.set_x_axis(results.q_x)
+            # fitH5.set_y_axis(results.q_y)
+            # fitH5.set_z_axis(results.q_z)
 
         self.__fitFile = self.__selectedFile
         self._setStatus(FitWidget.StatusCompleted)

kmap/io/FitH5.py

@@ -37,132 +37,294 @@ import numpy as np
 from .XsocsH5Base import XsocsH5Base
 
 
-class FitH5(XsocsH5Base):
-    scan_positions_path = 'scan_positions'
-    q_fit_path = 'q{0}fit'
-    status_path = 'success'
-    axis_path = 'axis/{0}'
-
-    @property
-    def scan_positions(self):
-        with self:
-            return self.sample_x, self.sample_y
-
-    sample_x = property(lambda self:
-                        self._get_array_data(FitH5.scan_positions_path + '/x'))
-
-    sample_y = property(lambda self:
-                        self._get_array_data(FitH5.scan_positions_path + '/y'))
-
-    x_fit = property(lambda self: self.__get_fit('x'))
-
-    y_fit = property(lambda self: self.__get_fit('y'))
-
-    z_fit = property(lambda self: self.__get_fit('z'))
-
-    x_height = property(lambda self: self.__get_data('x', 'height'))
-
-    y_height = property(lambda self: self.__get_data('y', 'height'))
-
-    z_height = property(lambda self: self.__get_data('z', 'height'))
-
-    x_center = property(lambda self: self.__get_data('x', 'center'))
-
-    y_center = property(lambda self: self.__get_data('y', 'center'))
-
-    z_center = property(lambda self: self.__get_data('z', 'center'))
-
-    x_width = property(lambda self: self.__get_data('x', 'width'))
-
-    y_width = property(lambda self: self.__get_data('y', 'width'))
-
-    z_width = property(lambda self: self.__get_data('z', 'width'))
-
-    status = property(lambda self: self._get_array_data(FitH5.status_path))
-
-    x_axis = property(lambda self: self.__get_axis_values('x'))
-
-    y_axis = property(lambda self: self.__get_axis_values('y'))
-
-    z_axis = property(lambda self: self.__get_axis_values('z'))
-
-    def __get_fit(self, axis):
-        with self:
-            height = self.__get_data(axis, 'height')
-            center = self.__get_data(axis, 'center')
-            width = self.__get_data(axis, 'width')
-        return height, center, width
+# class GaussianFitH5(FitH5):
 
-    def __get_data(self, axis, data):
-        data_path = FitH5.q_fit_path.format(axis) + '/{0}'.format(data)
-        return self._get_array_data(data_path)
-
-    def __get_axis_values(self, axis):
-        return self._get_array_data(FitH5.axis_path.format(axis))
-
-    def export_txt(self, filename):
-        with self:
-            with open(filename, 'w+') as res_f:
-                res_f.write('X Y '
-                            'height_x center_x width_x '
-                            'height_y center_y width_y '
-                            'height_z center_z width_z '
-                            '|q| status\n')
-                x_height, x_center, x_width = self.x_fit
-                y_height, y_center, y_width = self.y_fit
-                z_height, z_center, z_width = self.z_fit
-                q = np.sqrt(x_center ** 2 +
-                            y_center ** 2 +
-                            z_center ** 2)
-                status = self.status
-                x, y = self.scan_positions
-
-                for i, s in enumerate(status):
-                    r = [x[i], y[i],
-                         x_height[i], x_center[i], x_width[i],
-                         y_height[i], y_center[i], y_width[i],
-                         z_height[i], z_center[i], z_width[i],
-                         q[i], s]
-                    res_str = '{0}\n'.format(' '.join(str(e) for e in r))
-                    res_f.write(res_str)
+class FitH5(XsocsH5Base):
+    title_path = '{entry}/title'
+    start_time_path = '{entry}/start_time'
+    end_time_path = '{entry}/end_time'
+    date_path = '{entry}/{process}/date'
+    axis_path = '{entry}/{process}/axis'
+    configuration_path = '{entry}/{process}/configuration'
+    results_path = '{entry}/{process}/results'
+    qx_results_path = '{entry}/{process}/results/qx/{0}'
+    qy_results_path = '{entry}/{process}/results/qy/{0}'
+    qz_results_path = '{entry}/{process}/results/qz/{0}'
+
+    def __init__(self, h5_f, mode='r'):
+        super(XsocsH5Base, self).__init__(h5_f, mode=mode)
+
+        self.__entries = None
+
+    def title(self, entry):
+        with self._get_file() as h5_file:
+            path = entry + '/title'
+            return h5_file[path][()]
+
+    def _update_entries(self):
+        with self._get_file() as h5_file:
+            # TODO : this isnt pretty but for some reason the attrs.get() fails
+            # when there is no attribute NX_class (should return the default
+            # None)
+            self.__entries = sorted([key for key in h5_file
+                                     if ('NX_class' in h5_file[key].attrs and
+                                         h5_file[key].attrs['NX_class'] == 'NXentry')])  # noqa
+
+    def entries(self):
+        if self.__entries is None:
+            self._update_entries()
+        return self.__entries[:]
+
+    def processes(self, entry):
+        with self._get_file() as h5_file:
+            entry_grp = h5_file[entry]
+            processes = sorted([key for key in entry_grp
+                                if ('NX_class' in entry_grp[key].attrs and
+                                    h5_file[key].attrs[
+                                        'NX_class'] == 'NXprocess')])
+        return processes
+
+    def results(self, entry, process):
+        with self._get_file() as h5_file:
+            results_path = FitH5.results_path.format(entry=entry,
+                                                     process=process)
+            result_grp = h5_file[results_path]
+            results = sorted([key for key in result_grp])
+            return results
+
+    def result(self, entry, process, result):
+        result_path = FitH5.result_path.format(entry=entry,
+                                               process=process,
+                                               result=result)
+        return self._get_array_data(result_path)
 
 
 class FitH5Writer(FitH5):
 
-    def __init__(self, h5_f, mode='a', **kwargs):
-        super(FitH5Writer, self).__init__(h5_f, mode=mode, **kwargs)
-
-    def set_scan_positions(self, x, y):
-        path_tpl = FitH5.scan_positions_path + '/{0}'
-        self._set_array_data(path_tpl.format('x'), x)
-        self._set_array_data(path_tpl.format('y'), y)
-
-    def set_x_fit(self, height, center, width):
-        self.__set_fit('x', height, center, width)
-
-    def set_y_fit(self, height, center, width):
-        self.__set_fit('y', height, center, width)
-
-    def set_z_fit(self, height, center, width):
-        self.__set_fit('z', height, center, width)
-
-    def __set_fit(self, axis, height, center, width):
-        path_tpl = FitH5.q_fit_path.format(axis) + '/{0}'
-        self._set_array_data(path_tpl.format('height'), height)
-        self._set_array_data(path_tpl.format('center'), center)
-        self._set_array_data(path_tpl.format('width'), width)
-
-    def set_status(self, status):
-        self._set_array_data(FitH5.status_path, status)
+    def create_entry(self, entry):
+        with self._get_file() as h5_file:
+            # TODO : check if it already exists
+            entry_grp = h5_file.require_group(entry)
+            entry_grp.attrs['NX_class'] = np.string_('NXentry')
+            self._update_entries()
+
+    def create_process(self, entry, process):
+        # TODO : check that there isn't already an existing process
+        with self._get_file() as h5_file:
+            if entry not in h5_file:
+                self.create_entry(entry)
+            entry_grp = h5_file[entry]
+
+            # TODO : check if it exists
+            process_grp = entry_grp.require_group[process]
+            process_grp.attrs['NX_class'] = np.string_('NXprocess')
+            results_grp = process_grp.require_group('results')
+            results_grp.attrs['NX_class'] = np.string_('NXcollection')
+
+    def set_title(self, entry, title):
+        self._set_scalar_data(FitH5.title_path.format(entry), title)
+
+    def set_result(self, entry, process, name, data):
+        result_path = FitH5.result_path.format(entry=entry,
+                                               process=process,
+                                               result=name)
+        self._set_array_data(result_path, data)
+
+    #
+    # def export_txt(self, filename):
+    #     with self:
+    #         with open(filename, 'w+') as res_f:
+    #             res_f.write('X Y '
+    #                         'height_x center_x width_x '
+    #                         'height_y center_y width_y '
+    #                         'height_z center_z width_z '
+    #                         '|q| status\n')
+    #             x_height, x_center, x_width = self.x_fit
+    #             y_height, y_center, y_width = self.y_fit
+    #             z_height, z_center, z_width = self.z_fit
+    #             q = np.sqrt(x_center ** 2 +
+    #                         y_center ** 2 +
+    #                         z_center ** 2)
+    #             status = self.status
+    #             x, y = self.scan_positions
+    #
+    #             for i, s in enumerate(status):
+    #                 r = [x[i], y[i],
+    #                      x_height[i], x_center[i], x_width[i],
+    #                      y_height[i], y_center[i], y_width[i],
+    #                      z_height[i], z_center[i], z_width[i],
+    #                      q[i], s]
+    #                 res_str = '{0}\n'.format(' '.join(str(e) for e in r))
+    #                 res_f.write(res_str)
 
-    def __set_axis_values(self, axis, values):
-        self._set_array_data(FitH5.axis_path.format(axis), values)
-
-    def set_x_axis(self, values):
-        self.__set_axis_values('x', values)
+#
+# class FitH5Writer(FitH5):
+#
+#     def __init__(self, h5_f, mode='a', **kwargs):
+#         super(FitH5Writer, self).__init__(h5_f, mode=mode, **kwargs)
+#
+#     def set_scan_positions(self, x, y):
+#         path_tpl = FitH5.scan_positions_path + '/{0}'
+#         self._set_array_data(path_tpl.format('x'), x)
+#         self._set_array_data(path_tpl.format('y'), y)
+#
+#     def set_x_fit(self, height, center, width):
+#         self.__set_fit('x', height, center, width)
+#
+#     def set_y_fit(self, height, center, width):
+#         self.__set_fit('y', height, center, width)
+#
+#     def set_z_fit(self, height, center, width):
+#         self.__set_fit('z', height, center, width)
+#
+#     def __set_fit(self, axis, height, center, width):
+#         path_tpl = FitH5.q_fit_path.format(axis) + '/{0}'
+#         self._set_array_data(path_tpl.format('height'), height)
+#         self._set_array_data(path_tpl.format('center'), center)
+#         self._set_array_data(path_tpl.format('width'), width)
+#
+#     def set_status(self, status):
+#         self._set_array_data(FitH5.status_path, status)
+#
+#     def __set_axis_values(self, axis, values):
+#         self._set_array_data(FitH5.axis_path.format(axis), values)
+#
+#     def set_x_axis(self, values):
+#         self.__set_axis_values('x', values)
+#
+#     def set_y_axis(self, values):
+#         self.__set_axis_values('y', values)
+#
+#     def set_z_axis(self, values):
+#         self.__set_axis_values('z', values)
 
-    def set_y_axis(self, values):
-        self.__set_axis_values('y', values)
 
-    def set_z_axis(self, values):
-        self.__set_axis_values('z', values)
+# class FitH5(XsocsH5Base):
+#     scan_positions_path = 'scan_positions'
+#     q_fit_path = 'q{0}fit'
+#     status_path = 'success'
+#     axis_path = 'axis/{0}'
+#
+#     @property
+#     def scan_positions(self):
+#         with self:
+#             return self.sample_x, self.sample_y
+#
+#     sample_x = property(lambda self:
+#                         self._get_array_data(FitH5.scan_positions_path + '/x'))
+#
+#     sample_y = property(lambda self:
+#                         self._get_array_data(FitH5.scan_positions_path + '/y'))
+#
+#     x_fit = property(lambda self: self.__get_fit('x'))
+#
+#     y_fit = property(lambda self: self.__get_fit('y'))
+#
+#     z_fit = property(lambda self: self.__get_fit('z'))
+#
+#     x_height = property(lambda self: self.__get_data('x', 'height'))
+#
+#     y_height = property(lambda self: self.__get_data('y', 'height'))
+#
+#     z_height = property(lambda self: self.__get_data('z', 'height'))
+#
+#     x_center = property(lambda self: self.__get_data('x', 'center'))
+#
+#     y_center = property(lambda self: self.__get_data('y', 'center'))
+#
+#     z_center = property(lambda self: self.__get_data('z', 'center'))
+#
+#     x_width = property(lambda self: self.__get_data('x', 'width'))
+#
+#     y_width = property(lambda self: self.__get_data('y', 'width'))
+#
+#     z_width = property(lambda self: self.__get_data('z', 'width'))
+#
+#     status = property(lambda self: self._get_array_data(FitH5.status_path))
+#
+#     x_axis = property(lambda self: self.__get_axis_values('x'))
+#
+#     y_axis = property(lambda self: self.__get_axis_values('y'))
+#
+#     z_axis = property(lambda self: self.__get_axis_values('z'))
+#
+#     def __get_fit(self, axis):
+#         with self:
+#             height = self.__get_data(axis, 'height')
+#             center = self.__get_data(axis, 'center')
+#             width = self.__get_data(axis, 'width')
+#         return height, center, width
+#
+#     def __get_data(self, axis, data):
+#         data_path = FitH5.q_fit_path.format(axis) + '/{0}'.format(data)
+#         return self._get_array_data(data_path)
+#
+#     def __get_axis_values(self, axis):
+#         return self._get_array_data(FitH5.axis_path.format(axis))
+#
+#     def export_txt(self, filename):
+#         with self:
+#             with open(filename, 'w+') as res_f:
+#                 res_f.write('X Y '
+#                             'height_x center_x width_x '
+#                             'height_y center_y width_y '
+#                             'height_z center_z width_z '
+#                             '|q| status\n')
+#                 x_height, x_center, x_width = self.x_fit
+#                 y_height, y_center, y_width = self.y_fit
+#                 z_height, z_center, z_width = self.z_fit
+#                 q = np.sqrt(x_center ** 2 +
+#                             y_center ** 2 +
+#                             z_center ** 2)
+#                 status = self.status
+#                 x, y = self.scan_positions
+#
+#                 for i, s in enumerate(status):
+#                     r = [x[i], y[i],
+#                          x_height[i], x_center[i], x_width[i],
+#                          y_height[i], y_center[i], y_width[i],
+#                          z_height[i], z_center[i], z_width[i],
+#                          q[i], s]
+#                     res_str = '{0}\n'.format(' '.join(str(e) for e in r))
+#                     res_f.write(res_str)
+#
+#
+# class FitH5Writer(FitH5):
+#
+#     def __init__(self, h5_f, mode='a', **kwargs):
+#         super(FitH5Writer, self).__init__(h5_f, mode=mode, **kwargs)
+#
+#     def set_scan_positions(self, x, y):
+#         path_tpl = FitH5.scan_positions_path + '/{0}'
+#         self._set_array_data(path_tpl.format('x'), x)
+#         self._set_array_data(path_tpl.format('y'), y)
+#
+#     def set_x_fit(self, height, center, width):
+#         self.__set_fit('x', height, center, width)
+#
+#     def set_y_fit(self, height, center, width):
+#         self.__set_fit('y', height, center, width)
+#
+#     def set_z_fit(self, height, center, width):
+#         self.__set_fit('z', height, center, width)
+#
+#     def __set_fit(self, axis, height, center, width):
+#         path_tpl = FitH5.q_fit_path.format(axis) + '/{0}'
+#         self._set_array_data(path_tpl.format('height'), height)
+#         self._set_array_data(path_tpl.format('center'), center)
+#         self._set_array_data(path_tpl.format('width'), width)
+#
+#     def set_status(self, status):
+#         self._set_array_data(FitH5.status_path, status)
+#
+#     def __set_axis_values(self, axis, values):
+#         self._set_array_data(FitH5.axis_path.format(axis), values)
+#
+#     def set_x_axis(self, values):
+#         self.__set_axis_values('x', values)
+#
+#     def set_y_axis(self, values):
+#         self.__set_axis_values('y', values)
+#
+#     def set_z_axis(self, values):
+#         self.__set_axis_values('z', values)

kmap/io/XsocsH5.py

@@ -333,7 +333,7 @@ class XsocsH5Writer(XsocsH5):
             grp['info'] = det_grp
             det_grp['data'] = _h5py.SoftLink(self.img_data_tpl.format(entry))
 
-        self._update_entries()
+            self._update_entries()
 
 
 class XsocsH5MasterWriter(XsocsH5Writer):

kmap/process/peak_fit.py

@@ -55,7 +55,8 @@ FitResult = namedtuple('FitResult', ['sample_x', 'sample_y',
                                      'x_height', 'x_center', 'x_width',
                                      'y_height', 'y_center', 'y_width',
                                      'z_height', 'z_center', 'z_width',
-                                     'status'])
+                                     'status',
+                                     'fit_name'])
 
 _const_inv_2_pi_ = np.sqrt(2 * np.pi)
 
@@ -261,6 +262,11 @@ def peak_fit(qspace_f,
         q_y = q_y[ySlice]
         q_z = q_z[zSlice]
 
+    if fit_type == FitTypes.LEASTSQ:
+        fit_name = 'LeastSq'
+    else:
+        fit_name = 'Centroid'
+
     fit_results = FitResult(sample_x=x_pos,
                             sample_y=y_pos,
                             q_x=q_x,
@@ -275,7 +281,8 @@ def peak_fit(qspace_f,
                             z_height=results_np[:, 6].ravel(),
                             z_center=results_np[:, 7].ravel(),
                             z_width=results_np[:, 8].ravel(),
-                            status=status)
+                            status=status,
+                            fit_name=fit_name)
     return fit_results