Merge pull request #654 from stuart-cls/standard-map-vars

Standard map vars

orangecontrib/spectroscopy/io/agilent.py

@@ -9,6 +9,7 @@
     agilentMosaicTiles
 from orangecontrib.spectroscopy.io.util import SpectralFileFormat, _spectra_from_image, \
     TileFileFormat, ConstantBytesVisibleImage
+from orangecontrib.spectroscopy.utils import MAP_X_VAR, MAP_Y_VAR
 
 
 def load_visible_images(vis_img_list: list[dict]) -> list[ConstantBytesVisibleImage]:
@@ -213,8 +214,8 @@ def read_tile(self):
 
         attrs = [Orange.data.ContinuousVariable.make("%f" % f) for f in features]
         domain = Orange.data.Domain(attrs, None,
-                                    metas=[Orange.data.ContinuousVariable.make("map_x"),
-                                           Orange.data.ContinuousVariable.make("map_y")]
+                                    metas=[Orange.data.ContinuousVariable.make(MAP_X_VAR),
+                                           Orange.data.ContinuousVariable.make(MAP_Y_VAR)]
                                     )
 
         try:

orangecontrib/spectroscopy/io/ascii.py

@@ -5,6 +5,7 @@
 
 from orangecontrib.spectroscopy.util import getx
 from orangecontrib.spectroscopy.io.util import SpectralFileFormat
+from orangecontrib.spectroscopy.utils import MAP_X_VAR, MAP_Y_VAR
 
 
 class AsciiColReader(FileFormat, SpectralFileFormat):
@@ -57,7 +58,7 @@ def read(self):
             domain = Orange.data.Domain([ContinuousVariable.make("%f" % f) for f in dom_vals], None)
             tbl = np.loadtxt(f, ndmin=2)
             data = Table.from_numpy(domain, X=tbl[:, 2:])
-            metas = [ContinuousVariable.make('map_x'), ContinuousVariable.make('map_y')]
+            metas = [ContinuousVariable.make(MAP_X_VAR), ContinuousVariable.make(MAP_Y_VAR)]
             domain = Orange.data.Domain(domain.attributes, None, metas=metas)
             data = data.transform(domain)
             with data.unlocked(data.metas):
@@ -68,8 +69,8 @@ def read(self):
     @staticmethod
     def write_file(filename, data):
         wavelengths = getx(data)
-        map_x = data.domain["map_x"] if "map_x" in data.domain else ContinuousVariable("map_x")
-        map_y = data.domain["map_y"] if "map_y" in data.domain else ContinuousVariable("map_y")
+        map_x = data.domain[MAP_X_VAR] if MAP_X_VAR in data.domain else ContinuousVariable(MAP_X_VAR)
+        map_y = data.domain[MAP_Y_VAR] if MAP_Y_VAR in data.domain else ContinuousVariable(MAP_Y_VAR)
         ndom = Domain([map_x, map_y] + list(data.domain.attributes))
         data = data.transform(ndom)
         with open(filename, "wb") as f:

orangecontrib/spectroscopy/io/opus.py

@@ -5,9 +5,12 @@
 import numpy as np
 from Orange.data import FileFormat, ContinuousVariable, StringVariable, TimeVariable
 
+from orangecontrib.spectroscopy.utils import MAP_X_VAR, MAP_Y_VAR
+
 from .util import ConstantBytesVisibleImage
 
 
+
 class OPUSReader(FileFormat):
     """Reader for OPUS files"""
 
@@ -58,8 +61,8 @@ def read(self):
         if type(data) == opusFC.MultiRegionDataReturn:
             y_data = []
             meta_data = []
-            metas.extend([ContinuousVariable.make('map_x'),
-                          ContinuousVariable.make('map_y'),
+            metas.extend([ContinuousVariable.make(MAP_X_VAR),
+                          ContinuousVariable.make(MAP_Y_VAR),
                           StringVariable.make('map_region'),
                           TimeVariable.make('start_time')])
             for region in data.regions:
@@ -77,8 +80,8 @@ def read(self):
         elif type(data) == opusFC.MultiRegionTRCDataReturn:
             y_data = []
             meta_data = []
-            metas.extend([ContinuousVariable.make('map_x'),
-                          ContinuousVariable.make('map_y'),
+            metas.extend([ContinuousVariable.make(MAP_X_VAR),
+                          ContinuousVariable.make(MAP_Y_VAR),
                           StringVariable.make('map_region')])
             attrs = [ContinuousVariable.make(repr(data.labels[i]))
                      for i in range(len(data.labels))]
@@ -93,8 +96,8 @@ def read(self):
             meta_data = np.vstack(meta_data)
 
         elif type(data) == opusFC.ImageDataReturn:
-            metas.extend([ContinuousVariable.make('map_x'),
-                          ContinuousVariable.make('map_y')])
+            metas.extend([ContinuousVariable.make(MAP_X_VAR),
+                          ContinuousVariable.make(MAP_Y_VAR)])
 
             data_3D = data.spectra
 
@@ -109,8 +112,8 @@ def read(self):
                     meta_data = np.vstack((meta_data, coord))
 
         elif type(data) == opusFC.ImageTRCDataReturn:
-            metas.extend([ContinuousVariable.make('map_x'),
-                          ContinuousVariable.make('map_y')])
+            metas.extend([ContinuousVariable.make(MAP_X_VAR),
+                          ContinuousVariable.make(MAP_Y_VAR)])
 
             attrs = [ContinuousVariable.make(repr(data.labels[i]))
                      for i in range(len(data.labels))]

orangecontrib/spectroscopy/io/ptir.py

@@ -3,6 +3,7 @@
 from Orange.data import FileFormat
 
 from orangecontrib.spectroscopy.io.util import SpectralFileFormat, _spectra_from_image
+from orangecontrib.spectroscopy.utils import MAP_X_VAR, MAP_Y_VAR
 
 
 class PTIRFileReader(FileFormat, SpectralFileFormat):
@@ -174,8 +175,8 @@ def read_spectra(self):
             metas = np.array([x_locs[x_loc], y_locs[y_loc]]).T
 
             domain = Orange.data.Domain([], None,
-                                        metas=[Orange.data.ContinuousVariable.make("map_x"),
-                                               Orange.data.ContinuousVariable.make("map_y")]
+                                        metas=[Orange.data.ContinuousVariable.make(MAP_X_VAR),
+                                               Orange.data.ContinuousVariable.make(MAP_Y_VAR)]
                                         )
             data = Orange.data.Table.from_numpy(domain, X=np.zeros((len(spectra), 0)),
                                                 metas=np.asarray(metas, dtype=object))

orangecontrib/spectroscopy/io/util.py

@@ -3,6 +3,8 @@
 import numpy as np
 from Orange.data import Domain, ContinuousVariable, Table
 
+from orangecontrib.spectroscopy.utils import MAP_X_VAR, MAP_Y_VAR
+
 
 class SpectralFileFormat:
 
@@ -29,8 +31,8 @@ def _metatable_maplocs(x_locs, y_locs):
     metas = np.vstack((x_locs, y_locs)).T
 
     domain = Domain([], None,
-                    metas=[ContinuousVariable.make("map_x"),
-                           ContinuousVariable.make("map_y")]
+                    metas=[ContinuousVariable.make(MAP_X_VAR),
+                           ContinuousVariable.make(MAP_Y_VAR)]
                     )
     data = Table.from_numpy(domain, X=np.zeros((len(metas), 0)),
                             metas=np.asarray(metas, dtype=object))

orangecontrib/spectroscopy/utils/__init__.py

@@ -2,6 +2,9 @@
 
 from Orange.data import Domain, Table
 
+MAP_X_VAR = "map_x"
+MAP_Y_VAR = "map_y"
+
 
 def apply_columns_numpy(array, function, selector=None, chunk_size=10 ** 7, callback=None):
     """Split the array by columns, applies selection and then the function.