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Add a few workarounds to load new RDAs from Vida scanner #152

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Add a few workarounds to load new RDAs from Vida scanner #152

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19 changes: 15 additions & 4 deletions suspect/io/rda.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,10 +25,10 @@
"StationName", "InstitutionName", "DeviceSerialNumber", "InstanceDate",
"InstanceTime", "InstanceComments", "SequenceName", "SequenceDescription",
"Nucleus", "TransmitCoil", "PatientSex", "HammingFilter", "FrequencyCorrection"],
"float_arrays": ["PositionVector", "RowVector", "ColumnVector"],
"float_arrays": ["PositionVector", "RowVector", "ColumnVector","SlabThickness"],
"integer_arrays": ["CSIMatrixSize", "CSIMatrixSizeOfScan", "CSIGridShift"],
"string_arrays": ["SoftwareVersion"],
"dictionaries": ["TransmitRefAmplitude"]
"dictionaries": ["TransmitRefAmplitude","SlabOrientation","MidSlabPosition",""]
}


Expand All @@ -46,7 +46,7 @@ def load_rda(filename):
elif key in rda_types["integers"]:
header_dict[key] = int(value)
elif key in rda_types["floats"]:
header_dict[key] = float(value)
header_dict[key] = float(value.replace(",",".",1))
elif "[" in key and "]" in key:
# could be a dict or a list
key, index = re.split(r"\]|\[", key)[0:2]
Expand All @@ -57,7 +57,7 @@ def load_rda(filename):
else:
# not a dictionary, must be a list
if key in rda_types["float_arrays"]:
value = float(value)
value = float(value.replace(",",".",1))
elif key in rda_types["integer_arrays"]:
value = int(value)
index = int(index)
Expand Down Expand Up @@ -90,6 +90,17 @@ def load_rda(filename):
if "VOIReadoutFOV" not in header_dict:
if "VOIReadoutVOV" in header_dict:
header_dict["VOIReadoutFOV"] = header_dict.pop("VOIReadoutVOV")
#lazy workaround for new Viva scanner
elif "SlabOrientation" in header_dict:
header_dict["VOIReadoutFOV"] = 999.9
header_dict["VOIPhaseFOV"] = 999.9
header_dict["VOIThickness"] = 999.9
header_dict["VOIPositionSag"] = 999.9
header_dict["VOIPositionCor"] = 999.9
header_dict["VOIPositionTra"] = 999.9
#header_dict["PixelSpacingCol"] = 999.9
#header_dict["PixelSpacingRow"] = 999.9
header_dict["PixelSpacing3D"] = 999.9

# combine positional elements in the header
voi_size = (header_dict["VOIReadoutFOV"],
Expand Down