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Robust writing of with missing header values #76

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Robust writing of with missing header values #76

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9db2a84
added try around getattr to avoid libe57 exception
mitch-galea Feb 16, 2023
7dcc6c7
fixed error in get_attr_try
mitch-galea Feb 16, 2023
a26c0fc
initial value is min row/col
mitch-galea Feb 16, 2023
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34 changes: 20 additions & 14 deletions src/pye57/e57.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,12 @@
class WindowsError(OSError):
pass

def get_attr_try(object, attribute, default):
"""wraps get_attr_try in try to avoid libe57 exception when attribute is missing"""
try:
return getattr(object, attribute, default)
except libe57.E57Exception:
return default

SUPPORTED_CARTESIAN_POINT_FIELDS = {
"cartesianX": "d",
Expand Down Expand Up @@ -223,17 +229,17 @@ def write_scan_raw(self, data: Dict, *, name=None, rotation=None, translation=No
raise ValueError("Unsupported point field: %s" % field)

if rotation is None:
rotation = getattr(scan_header, "rotation", np.array([1, 0, 0, 0]))
rotation = get_attr_try(scan_header, "rotation", np.array([1, 0, 0, 0]))

if translation is None:
translation = getattr(scan_header, "translation", np.array([0, 0, 0]))
translation = get_attr_try(scan_header, "translation", np.array([0, 0, 0]))

if name is None:
name = getattr(scan_header, "name", "Scan %s" % len(self.data3d))
name = get_attr_try(scan_header, "name", "Scan %s" % len(self.data3d))

temperature = getattr(scan_header, "temperature", 0)
relativeHumidity = getattr(scan_header, "relativeHumidity", 0)
atmosphericPressure = getattr(scan_header, "atmosphericPressure", 0)
temperature = get_attr_try(scan_header, "temperature", 0)
relativeHumidity = get_attr_try(scan_header, "relativeHumidity", 0)
atmosphericPressure = get_attr_try(scan_header, "atmosphericPressure", 0)

scan_node = libe57.StructureNode(self.image_file)
scan_node.set("guid", libe57.StringNode(self.image_file, "{%s}" % uuid.uuid4()))
Expand Down Expand Up @@ -265,8 +271,8 @@ def write_scan_raw(self, data: Dict, *, name=None, rotation=None, translation=No
scan_node.set("indexBounds", ibox)

if "intensity" in data:
int_min = getattr(scan_header, "intensityMinimum", np.min(data["intensity"]))
int_max = getattr(scan_header, "intensityMaximum", np.max(data["intensity"]))
int_min = get_attr_try(scan_header, "intensityMinimum", np.min(data["intensity"]))
int_max = get_attr_try(scan_header, "intensityMaximum", np.max(data["intensity"]))
intbox = libe57.StructureNode(self.image_file)
intbox.set("intensityMinimum", libe57.FloatNode(self.image_file, int_min))
intbox.set("intensityMaximum", libe57.FloatNode(self.image_file, int_max))
Expand Down Expand Up @@ -323,10 +329,10 @@ def write_scan_raw(self, data: Dict, *, name=None, rotation=None, translation=No
translation_node.set("z", libe57.FloatNode(self.image_file, translation[2]))
pose_node.set("translation", translation_node)

start_datetime = getattr(scan_header, "acquisitionStart_dateTimeValue", 0)
start_atomic = getattr(scan_header, "acquisitionStart_isAtomicClockReferenced", False)
end_datetime = getattr(scan_header, "acquisitionEnd_dateTimeValue", 0)
end_atomic = getattr(scan_header, "acquisitionEnd_isAtomicClockReferenced", False)
start_datetime = get_attr_try(scan_header, "acquisitionStart_dateTimeValue", 0)
start_atomic = get_attr_try(scan_header, "acquisitionStart_isAtomicClockReferenced", False)
end_datetime = get_attr_try(scan_header, "acquisitionEnd_dateTimeValue", 0)
end_atomic = get_attr_try(scan_header, "acquisitionEnd_isAtomicClockReferenced", False)
acquisition_start = libe57.StructureNode(self.image_file)
scan_node.set("acquisitionStart", acquisition_start)
acquisition_start.set("dateTimeValue", libe57.FloatNode(self.image_file, start_datetime))
Expand Down Expand Up @@ -376,9 +382,9 @@ def write_scan_raw(self, data: Dict, *, name=None, rotation=None, translation=No
max_row = np.max(data["rowIndex"])
min_col = np.min(data["columnIndex"])
max_col = np.max(data["columnIndex"])
points_prototype.set("rowIndex", libe57.IntegerNode(self.image_file, 0, min_row, max_row))
points_prototype.set("rowIndex", libe57.IntegerNode(self.image_file, min_row, min_row, max_row))
field_names.append("rowIndex")
points_prototype.set("columnIndex", libe57.IntegerNode(self.image_file, 0, min_col, max_col))
points_prototype.set("columnIndex", libe57.IntegerNode(self.image_file, min_col, min_col, max_col))
field_names.append("columnIndex")

if "cartesianInvalidState" in data:
Expand Down
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