26 reader for brml brucker files #43
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ka-sarthak
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hampusnasstrom
approved these changes
Dec 8, 2023
| @@ -259,7 +260,7 @@ def get_1d_scan(self, logger: BoundLogger=None): | |||
| if not self.data.shape[0] == 1: | |||
| if logger is not None: | |||
| logger.warning( | |||
| 'Multiple/2D scan currently not supported. ' | |||
| 'Multiple/2D/RSM scan currently not supported. ' | |||
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Did you intend to also change the RASX reader now?
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Ah, yeah, I agree it's not the best practice. But as it is a minor change to keep the warning message same for the two readers, i thought of pushing it here.
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| class BRMLfile(object): | ||
| def __init__(self, path, exp_nbr=0, encoding="utf-8", verbose=True): | ||
| self.path = path | ||
| with zipfile.ZipFile(path, 'r') as fh: | ||
| experiment = "Experiment%i"%exp_nbr | ||
| datacontainer = "%s/DataContainer.xml"%experiment | ||
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|
||
| with fh.open(datacontainer, "r") as xml: | ||
| data = xmltodict.parse(xml.read(), encoding=encoding) | ||
| rawlist = data["DataContainer"]["RawDataReferenceList"]["string"] | ||
| # rawlist contains the reference to all the raw files (multiple in case of RSM) | ||
| if not isinstance(rawlist, list): | ||
| rawlist = [rawlist] | ||
|
|
||
| self.data = collections.defaultdict(list) | ||
| self.motors = self.data # collections.defaultdict(list) | ||
| for i, rawpath in enumerate(rawlist): | ||
| if verbose: | ||
| if not i: | ||
| print("Loading frame %i"%i, end="") | ||
| else: | ||
| print(", %i"%i, end="") | ||
| with fh.open(rawpath, "r") as xml: | ||
| # entering RawData<int>.xml | ||
| data = xmltodict.parse(xml.read(), encoding=encoding) | ||
| dataroute = data["RawData"]["DataRoutes"]["DataRoute"] | ||
| scaninfo = dataroute["ScanInformation"] | ||
| nsteps = int(scaninfo["MeasurementPoints"]) | ||
| if nsteps==1: | ||
| rawdata = np.array(dataroute["Datum"].split(",")) | ||
| elif nsteps>1: | ||
| rawdata = np.array([d.split(",") for d in dataroute["Datum"]]) | ||
|
|
||
| rawdata = rawdata.astype(float).T | ||
| rdv = dataroute["DataViews"]["RawDataView"] | ||
| for view in rdv: | ||
| viewtype = view["@xsi:type"] | ||
| vstart = int(view["@Start"]) | ||
| vlen = int(view["@Length"]) | ||
| if viewtype=="FixedRawDataView": | ||
| vname = view["@LogicName"] | ||
| self.data[vname].append(rawdata[vstart:(vstart+vlen)]) | ||
| elif viewtype=="RecordedRawDataView": | ||
| vname = view["Recording"]["@LogicName"] | ||
| self.data[vname].append(rawdata[vstart:(vstart+vlen)]) | ||
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||
| self.data["ScanName"].append(scaninfo["@ScanName"]) | ||
| self.data["TimePerStep"].append(scaninfo["TimePerStep"]) | ||
| self.data["TimePerStepEffective"].append(scaninfo["TimePerStepEffective"]) | ||
| self.data["ScanMode"].append(scaninfo["ScanMode"]) | ||
|
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||
| scanaxes = scaninfo["ScanAxes"]["ScanAxisInfo"] | ||
| if not isinstance(scanaxes, list): | ||
| scanaxes = [scanaxes] | ||
| for axis in scanaxes: | ||
| aname = axis["@AxisName"] | ||
| aunit = axis["Unit"]["@Base"] | ||
| aref = float(axis["Reference"]) | ||
| astart = float(axis["Start"]) + aref | ||
| astop = float(axis["Stop"]) + aref | ||
| astep = float(axis["Increment"]) | ||
| nint = int(round(abs(astop-astart)/astep)) | ||
| adata = {} # not originally part of Carsten's code | ||
| adata["Value"] = np.linspace(astart, astop, nint+1) | ||
| adata["Unit"] = aunit.lower() | ||
| self.data[aname].append(adata) | ||
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||
| drives = data["RawData"]["FixedInformation"]["Drives"]["InfoData"] | ||
| for axis in drives: | ||
| aname = axis["@LogicName"] | ||
| apos = float(axis["Position"]["@Value"]) | ||
| aunit = axis["Position"]["@Unit"] | ||
| adata = {} # not originally part of Carsten's code | ||
| adata["Value"] = apos | ||
| adata["Unit"] = aunit.lower() | ||
| self.motors[aname].append(adata) | ||
|
|
||
| # (block starts) not originally part of Carsten's code | ||
| try: | ||
| self.mounted_optics_info = ( | ||
| data["RawData"]["FixedInformation"]["Instrument"] | ||
| ["PrimaryTracks"]["TrackInfoData"]["MountedOptics"]["InfoData"] | ||
| ) | ||
| except (KeyError, TypeError): | ||
| self.mounted_optics_info = [] | ||
| # (block end) not originally part of Carsten's code | ||
|
|
||
| for key in self.data: | ||
| self.data[key] = np.array(self.data[key]).squeeze() | ||
| if not self.data[key].shape: | ||
| self.data[key] = self.data[key].item() | ||
| for key in self.motors: | ||
| self.motors[key] = np.array(self.motors[key]).squeeze() | ||
| if not self.motors[key].shape: | ||
| self.motors[key] = self.motors[key].item() |
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I'm guessing this part is from Carsten so I only skimmed through it. Let me know if you want me to look closer at it.
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Correct, and I have tried to keep most of the code from Carsten as it is. So you can skim though it.
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| Dict[str, Any]: Each dict item contains a list with numerical value | ||
| (numpy.ndarray) at index 0 and unit (str) at index 1. If quantity | ||
| is not available, the dict item will default to []. If units are not | ||
| available for two_theta or axis positions, they will default to 'deg'. |
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This is fine but just out of curiosity, why do you not just return the pint.Quantity directly?
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Yeah, we could do that but I did not want to introduce any nomad functionality (ureg in this case) in IKZ.py.
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| def set_quantity(value: Any=None, unit: str=None) -> Any: | ||
| ''' | ||
| Sets the quantity based on whether value or/and unit are available. | ||
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|
||
| Args: | ||
| value (Any): Value of the quantity. | ||
| unit (str): Unit of the quantity. | ||
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| Returns: | ||
| Any: Processed quantity with datatype depending on the value. | ||
| ''' | ||
| if not unit: | ||
| return value | ||
| return value * ureg(unit) |
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This is repeated from above. I would say that we either extract this function out or like I commented in the IKZ.py we could move the unit addition in there.
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Yes, indeed. I was thinking about moving this function to nomad_measurements/utils.py after merging this commit. Or we could also put this function elsewhere.
Closed
6 tasks
|
Thanks Hampus! It is indeed an important point about the units and we can make it better in next commits. For now, let's go ahead with merging this. |
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