Remove deprecated record_by metadata

rsciio/blockfile/_api.py

@@ -295,6 +295,7 @@ def file_reader(filename, lazy=False, mmap_mode=None, endianess="<"):
 
     units = ["nm", "nm", "cm", "cm"]
     names = ["y", "x", "dy", "dx"]
+    navigate = [True, True, False, False]
     scales = [header["SY"], header["SX"], SDP, SDP]
     date, time, time_zone = serial_date_to_ISO_format(header["Acquisition_time"])
     metadata = {
@@ -305,10 +306,7 @@ def file_reader(filename, lazy=False, mmap_mode=None, endianess="<"):
             "time_zone": time_zone,
             "notes": header["Note"],
         },
-        "Signal": {
-            "signal_type": "diffraction",
-            "record_by": "image",
-        },
+        "Signal": {"signal_type": "diffraction"},
     }
     # Create the axis objects for each axis
     dim = data.ndim
@@ -320,6 +318,7 @@ def file_reader(filename, lazy=False, mmap_mode=None, endianess="<"):
             "scale": scales[i],
             "offset": 0.0,
             "units": units[i],
+            "navigate": navigate[i],
         }
         for i in range(dim)
     ]

rsciio/bruker/_api.py

@@ -667,7 +667,7 @@ def _parse_image(self, xml_node, overview=False):
                 item["data"] = data
                 item["axes"][0]["size"] = image.height
                 item["axes"][1]["size"] = image.width
-                item["metadata"]["Signal"] = {"record_by": "image"}
+                item["metadata"]["Signal"] = {}
                 item["metadata"]["General"] = {}
                 if desc is not None:
                     item["metadata"]["General"]["title"] = str(desc.text)
@@ -1015,6 +1015,7 @@ def spx_reader(filename, lazy=False):
                 "offset": spectrum.offset,
                 "scale": spectrum.scale,
                 "units": "keV",
+                "navigate": False,
             }
         ],
         "metadata":
@@ -1036,7 +1037,6 @@ def spx_reader(filename, lazy=False):
             "Sample": {"name": name},
             "Signal": {
                 "signal_type": "EDS_%s" % mode,
-                "record_by": "spectrum",
                 "quantity": "X-rays (Counts)",
             },
         },
@@ -1427,20 +1427,23 @@ def bcf_hyperspectra(
                         "offset": 0,
                         "scale": obj_bcf.header.y_res * downsample,
                         "units": obj_bcf.header.units,
+                        "navigate": True,
                     },
                     {
                         "name": "width",
                         "size": hypermap.shape[1],
                         "offset": 0,
                         "scale": obj_bcf.header.y_res * downsample,
                         "units": obj_bcf.header.units,
+                        "navigate": True,
                     },
                     {
                         "name": "Energy",
                         "size": hypermap.shape[2],
                         "offset": eds_metadata.offset,
                         "scale": eds_metadata.scale,
                         "units": "keV",
+                        "navigate": False,
                     },
                 ],
                 "metadata":
@@ -1465,7 +1468,6 @@ def bcf_hyperspectra(
                     },
                     "Signal": {
                         "signal_type": "EDS_%s" % mode,
-                        "record_by": "spectrum",
                         "quantity": "X-rays (Counts)",
                     },
                 },

rsciio/digitalmicrograph/_api.py

@@ -449,7 +449,6 @@ def __init__(self, imdict, file, order="C"):
         self.imdict = Box(imdict, box_dots=True)
         self.file = file
         self._order = order if order else "C"
-        self._record_by = None
 
     @property
     def shape(self):
@@ -521,11 +520,10 @@ def title(self):
         return title if title else ""
 
     @property
-    def record_by(self):
-        if self._record_by is not None:
-            return self._record_by
+    def navigate(self):
+        result = [True] * len(self.shape)
         if len(self.scales) == 1:
-            return "spectrum"
+            result[-1] = False
         elif (
             (
                 self.imdict.get("ImageTags.Meta Data.Format") is not None
@@ -534,9 +532,10 @@ def record_by(self):
             )
             or (self.imdict.get("ImageTags.spim") is not None)
         ) and len(self.scales) == 2:
-            return "spectrum"
+            result[-1] = False
         else:
-            return "image"
+            result[-2:] = (False, False)
+        return result
 
     @property
     def to_spectrum(self):
@@ -733,9 +732,17 @@ def get_axes_dict(self):
                 "scale": scale,
                 "offset": offset,
                 "units": str(units),
+                "navigate": nav,
             }
-            for i, (name, size, scale, offset, units) in enumerate(
-                zip(self.names, self.shape, self.scales, self.offsets, self.units)
+            for i, (name, size, scale, offset, units, nav) in enumerate(
+                zip(
+                    self.names,
+                    self.shape,
+                    self.scales,
+                    self.offsets,
+                    self.units,
+                    self.navigate,
+                )
             )
         ]
 
@@ -747,7 +754,6 @@ def get_metadata(self, metadata=None):
         if "Signal" not in metadata:
             metadata["Signal"] = {}
         metadata["General"]["title"] = self.title
-        metadata["Signal"]["record_by"] = self.record_by
         metadata["Signal"]["signal_type"] = self.signal_type
         return metadata
 

rsciio/edax/_api.py

@@ -732,6 +732,7 @@ def spc_reader(filename, lazy=False, endianess="<", load_all_spc=False, **kwargs
         "scale": original_metadata["spc_header"]["evPerChan"] / 1000.0,
         "offset": original_metadata["spc_header"]["startEnergy"],
         "units": "keV",
+        "navigate": False,
     }
 
     # Assign metadata for spectrum:
@@ -742,7 +743,6 @@ def spc_reader(filename, lazy=False, endianess="<", load_all_spc=False, **kwargs
         },
         "Signal": {
             "signal_type": "EDS_SEM",
-            "record_by": "spectrum",
         },
     }
     metadata = _add_spc_metadata(metadata, spc_dict)
@@ -897,6 +897,7 @@ def spd_reader(
         else 1,
         "offset": original_metadata["spc_header"]["startEnergy"] if read_spc else 1,
         "units": "keV" if read_spc else None,
+        "navigate": False,
     }
 
     nav_units = "µm"
@@ -908,6 +909,7 @@ def spd_reader(
         "scale": original_metadata["ipr_header"]["mppX"] if read_ipr else 1,
         "offset": 0,
         "units": nav_units if read_ipr else None,
+        "navigate": True,
     }
 
     y_axis = {
@@ -917,6 +919,7 @@ def spd_reader(
         "scale": original_metadata["ipr_header"]["mppY"] if read_ipr else 1,
         "offset": 0,
         "units": nav_units if read_ipr else None,
+        "navigate": True,
     }
 
     # Assign metadata for spectrum image:
@@ -927,7 +930,6 @@ def spd_reader(
         },
         "Signal": {
             "signal_type": "EDS_SEM",
-            "record_by": "spectrum",
         },
     }
 

rsciio/empad/_api.py

@@ -59,7 +59,6 @@ def _parse_xml(filename):
         "width": 128,
         "height": 128,
         "raw_height": 130,
-        "record-by": "image",
     }
     if om.has_item("root.scan_parameters.series_count"):
         # Stack of images
@@ -113,7 +112,7 @@ def file_reader(filename, lazy=False, **kwds):
             "original_filename": fname,
             "title": os.path.splitext(fname)[0],
         },
-        "Signal": {"signal_type": "electron_diffraction", "record_by": "image"},
+        "Signal": {"signal_type": "electron_diffraction"},
     }
 
     if om.has_item("root.timestamp.isoformat"):
@@ -132,12 +131,14 @@ def file_reader(filename, lazy=False, **kwds):
     axes = []
     index_in_array = 0
     names = ["height", "width"]
+    navigate = [False, False]
 
     if "series_count" in info.keys():
         names = ["series_count"] + names
         units.insert(0, "ms")
         scales.insert(0, 1)
         origins.insert(0, 0)
+        navigate.insert(0, True)
     else:
         names = ["scan_x", "scan_y"] + names
         units.insert(0, "")
@@ -146,6 +147,8 @@ def file_reader(filename, lazy=False, **kwds):
         scales.insert(0, 1)
         origins.insert(0, 0)
         origins.insert(0, 0)
+        navigate.insert(0, True)
+        navigate.insert(0, True)
 
     sizes = [info[name] for name in names]
 
@@ -178,6 +181,7 @@ def file_reader(filename, lazy=False, **kwds):
                     "scale": scales[i],
                     "offset": origins[i] * scales[i],
                     "units": units[i],
+                    "navigate": navigate[i],
                 }
             )
             index_in_array += 1

rsciio/image/_api.py

@@ -232,10 +232,7 @@ def file_reader(filename, **kwds):
             "data": dc,
             "metadata": {
                 "General": {"original_filename": os.path.split(filename)[1]},
-                "Signal": {
-                    "signal_type": "",
-                    "record_by": "image",
-                },
+                "Signal": {"signal_type": ""},
             },
         }
     ]

rsciio/jeol/_api.py

@@ -198,13 +198,15 @@ def _read_img(filename, **kwargs):
             "offset": 0,
             "scale": yscale,
             "units": units,
+            "navigate": False,
         },
         {
             "name": "x",
             "size": width,
             "offset": 0,
             "scale": xscale,
             "units": units,
+            "navigate": False,
         },
     ]
 
@@ -228,9 +230,7 @@ def _read_img(filename, **kwargs):
             "time": datefile.time().isoformat(),
             "title": header_long["Image"]["Title"],
         },
-        "Signal": {
-            "record_by": "image",
-        },
+        "Signal": {},
     }
 
     dictionary = {
@@ -494,6 +494,7 @@ def _check_divisor(factor, number, string):
                     "offset": 0,
                     "scale": pixel_time * height * width / 1e3,
                     "units": "s",
+                    "navigate": True,
                 }
             ]
             width = data.shape[2]
@@ -506,24 +507,29 @@ def _check_divisor(factor, number, string):
                     "offset": origin[1],
                     "scale": yscale,
                     "units": units,
+                    "navigate": False,
                 },
                 {
                     "name": "x",
                     "size": width,
                     "offset": origin[0],
                     "scale": xscale,
                     "units": units,
+                    "navigate": False,
                 },
             ]
         )
         axes = axes_em.copy()
+        for ax in axes:
+            ax["navigate"] = True
         axes.append(
             {
                 "name": "Energy",
                 "size": channel_number,
                 "offset": energy_offset,
                 "scale": energy_scale,
                 "units": "keV",
+                "navigate": False,
             },
         )
         if (not last_valid) and only_valid_data:
@@ -561,7 +567,6 @@ def _check_divisor(factor, number, string):
                 "title": "EDS extracted from " + os.path.basename(filename),
             },
             "Signal": {
-                "record_by": "spectrum",
                 "quantity": "X-rays (Counts)",
                 "signal_type": "EDS_" + mode,
             },
@@ -579,9 +584,7 @@ def _check_divisor(factor, number, string):
                 "time": datefile.time().isoformat(),
                 "title": "S(T)EM Image extracted from " + os.path.basename(filename),
             },
-            "Signal": {
-                "record_by": "image",
-            },
+            "Signal": {},
         }
 
         image_list = [
@@ -1391,6 +1394,7 @@ def _read_eds(filename, **kwargs):
             "offset": header["CoefB"],
             "scale": header["CoefA"],
             "units": "keV",
+            "navigate": False,
         }
     ]
 
@@ -1416,7 +1420,6 @@ def _read_eds(filename, **kwargs):
             "title": "EDX",
         },
         "Signal": {
-            "record_by": "spectrum",
             "quantity": "X-rays (Counts)",
             "signal_type": "EDS_" + mode,
         },

rsciio/mrc/_api.py

@@ -219,12 +219,10 @@ def file_reader(filename, lazy=False, mmap_mode=None, endianess="<", **kwds):
 
     units = [None, "nm", "nm"]
     names = ["z", "y", "x"]
+    navigate = [True, False, False]
     metadata = {
         "General": {"original_filename": os.path.split(filename)[1]},
-        "Signal": {
-            "signal_type": "",
-            "record_by": "image",
-        },
+        "Signal": {"signal_type": ""},
     }
     # create the axis objects for each axis
     axes = [
@@ -235,6 +233,7 @@ def file_reader(filename, lazy=False, mmap_mode=None, endianess="<", **kwds):
             "scale": scales[i + 3 - dim],
             "offset": offsets[i + 3 - dim],
             "units": units[i + 3 - dim],
+            "navigate": navigate[i + 3 - dim],
         }
         for i in range(dim)
     ]

rsciio/msa/_api.py

@@ -284,11 +284,11 @@ def parse_msa_string(string, filename=None):
             "scale": parameters["XPERCHAN"] if "XPERCHAN" in parameters else 1,
             "offset": parameters["OFFSET"] if "OFFSET" in parameters else 0,
             "units": parameters["XUNITS"] if "XUNITS" in parameters else "",
+            "navigate": False,
         }
     ]
     if filename is not None:
         mapped.set_item("General.original_filename", os.path.split(filename)[1])
-    mapped.set_item("Signal.record_by", "spectrum")
     if "SIGNALTYPE" in parameters and parameters["SIGNALTYPE"]:
         if parameters["SIGNALTYPE"] == "ELS":
             mapped.set_item("Signal.signal_type", "EELS")