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bugfix release: pshell import and preview

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changes:
- catch runtime errors due to empty datasets
- improve window titles and graph names
- fix scaling of scienta image from XPSSpectrum script
- remove unnecessary spaces and underscores from folder names
This commit is contained in:
muntwiler_m
2016-09-22 14:15:09 +02:00
parent a87975d1e6
commit 0dc6ca820b
4 changed files with 324 additions and 96 deletions
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256
pearl/pearl-pshell-import.ipf
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@ -183,7 +183,9 @@ function /s psh5_load_complete(ANickName, APathName, AFileName, [load_data, load
for (ig = 0; ig < ng; ig += 1)
sg = StringFromList(ig, s_scanpaths, ";")
folder = CleanupName(ReplaceString("/", sg, ""), 0)
folder = ReplaceString("/", sg, "")
folder = ReplaceString(" ", folder, "")
folder = CleanupName(folder, 0)
setdatafolder fileDF
newdatafolder /s /o $folder
psh5_load_scan_complete(fileID, sg, load_data=load_data, load_attr=load_attr)
@ -219,14 +221,26 @@ end
/// @param load_attr 1 (default): load attributes; 0: do not load attributes
/// note: for correct scaling of the image, the attributes need to be loaded
///
/// @param pref_scans semicolon-separated list of preferred scans.
/// the items of the list are match strings for the Igor StringMatch function.
/// the first matching scan (i.e. top-level HDF5 group with a matching name) is loaded from the file.
/// if no match is found, the first scan is loaded.
///
/// @param pref_datasets semicolon-separated list of preferred datasets.
/// the items of the list are match strings for the Igor StringMatch function.
/// the first matching dataset is loaded from the file.
/// if no match is found, the first dataset listed in the file is loaded.
///
/// @return name of loaded preview wave.
///
function /s psh5_load_preview(ANickName, APathName, AFileName, [load_data, load_attr])
function /s psh5_load_preview(ANickName, APathName, AFileName, [load_data, load_attr, pref_scans, pref_datasets])
string ANickName
string APathName
string AFileName
variable load_data
variable load_attr
string pref_scans
string pref_datasets
if (ParamIsDefault(load_data))
load_data = 1
@ -234,7 +248,13 @@ function /s psh5_load_preview(ANickName, APathName, AFileName, [load_data, load_
if (ParamIsDefault(load_attr))
load_attr = 1
endif
if (ParamIsDefault(pref_scans))
pref_scans = "*scan1*;"
endif
if (ParamIsDefault(pref_datasets))
pref_datasets = ""
endif
dfref saveDF = GetDataFolderDFR()
setdatafolder root:
newdatafolder /o/s pearl_area
@ -253,12 +273,35 @@ function /s psh5_load_preview(ANickName, APathName, AFileName, [load_data, load_
if (v_flag == 0)
AFileName = s_path + s_filename
dfref fileDF = GetDataFolderDFR()
scanpaths = psh5_list_scans(fileID)
variable ng = ItemsInList(scanpaths)
variable ig
string sg
ig = 0
sg = StringFromList(ig, scanpaths, ";")
dataname = psh5_load_scan_preview(fileID, sg, set_scale=load_attr)
variable np = ItemsInList(pref_scans)
variable ip
string sp
variable found = 0
if (ng > 0)
for (ip = 0; ip < np; ip += 1)
for (ig = 0; ig < ng; ig += 1)
sg = StringFromList(ig, scanpaths)
sp = StringFromList(ip, pref_scans)
if (StringMatch(sg, sp))
found = 1
break
endif
endfor
if (found)
break
endif
endfor
if (!found)
ig = 0
endif
sg = StringFromList(ig, scanpaths)
dataname = psh5_load_scan_preview(fileID, sg, set_scale=load_attr, pref_datasets=pref_datasets)
endif
wave /z data = $dataname
string destpath = GetDataFolder(1, saveDF) + ANickName
@ -396,6 +439,9 @@ end
///
/// data is loaded into the current data folder.
///
/// this function does not scale the datasets.
/// call ps_scale_datasets() separately.
///
/// @param fileID ID of open HDF5 file from psh5_open_file().
///
/// @param scanpath path to the scan group in the HDF5 file, e.g. "/scan 1".
@ -517,28 +563,29 @@ function /s psh5_load_scan_meta(fileID, scanpath)
HDF5LoadData /O /Q /Z /A="Dimensions" /N=ScanDimensions /TYPE=1 fileID, scanpath
if (!v_flag)
wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
HDF5LoadData /O /Q /Z /A="Writables" /N=ScanWritables /TYPE=1 fileID, scanpath
if (!v_flag)
wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
endif
HDF5LoadData /O /Q /Z /A="Readables" /N=ScanReadables /TYPE=1 fileID, scanpath
if (!v_flag)
wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
endif
HDF5LoadData /O /Q /Z /A="Steps" /N=ScanSteps /TYPE=1 fileID, scanpath
if (!v_flag)
wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
endif
else
make /n=1 /o ScanDimensions
ScanDimensions = 0
wavenames = AddListItem("ScanDimensions", wavenames, ";", inf)
endif
HDF5LoadData /O /Q /Z /A="Readables" /N=ScanReadables /TYPE=1 fileID, scanpath
if (!v_flag)
wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
else
make /n=1 /o /t ScanReadables
ScanReadables[0] = "ScientaSpectrum"
wavenames = AddListItem("ScanReadables", wavenames, ";", inf)
endif
HDF5LoadData /O /Q /Z /A="Writables" /N=ScanWritables /TYPE=1 fileID, scanpath
if (!v_flag)
wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
endif
HDF5LoadData /O /Q /Z /A="Steps" /N=ScanSteps /TYPE=1 fileID, scanpath
if (!v_flag)
wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
endif
wavenames = ReplaceString(";;", wavenames, ";")
return wavenames
end
@ -573,6 +620,10 @@ function /s psh5_load_dataset(fileID, scanpath, datasetname, [set_scale])
string datasetname
variable set_scale
if (ParamIsDefault(set_scale))
set_scale = 1
endif
string datasetpath
datasetpath = scanpath + "/" + datasetname
datasetpath = ReplaceString("//", datasetpath, "/")
@ -586,7 +637,7 @@ function /s psh5_load_dataset(fileID, scanpath, datasetname, [set_scale])
endif
string dataname
if (di.ndims < 3)
if (di.ndims < 2)
HDF5LoadData /O /Q /Z fileID, datasetpath
dataname = StringFromList(0, S_waveNames)
else
@ -626,42 +677,68 @@ end
/// @arg 1 (default) set the wave scaling.
/// @arg 0 do not set the wave scaling.
///
/// @param pref_datasets semicolon-separated list of preferred datasets.
/// the items of the list are match strings for the Igor StringMatch function.
/// the first matching dataset is loaded from the file.
/// if no match is found, the first dataset listed in the file is loaded.
/// if empty, a hard-coded default preference list is used.
///
/// @return name of loaded wave if successful. empty string otherwise.
///
function /s psh5_load_scan_preview(fileID, scanpath, [set_scale])
function /s psh5_load_scan_preview(fileID, scanpath, [set_scale, pref_datasets])
variable fileID
string scanpath
variable set_scale
string pref_datasets
if (ParamIsDefault(set_scale))
set_scale = 1
endif
if (ParamIsDefault(pref_datasets) || (strlen(pref_datasets) == 0))
pref_datasets = "ScientaImage;ScientaSpectrum;ImageAngleDistribution;ImageEnergyDistribution;Counts;SampleCurrent"
endif
dfref saveDF = GetDataFolderDFR()
dfref dataDF = saveDF
string datasets = psh5_list_scan_datasets(fileID, scanpath)
string datasetname = ""
variable index
// todo: this should be generalized
if (strsearch(datasets, "ScientaImage", 0) >= 0)
datasetname = "ScientaImage"
elseif (strsearch(datasets, "ScientaSpectrum", 0) >= 0)
datasetname = "ScientaSpectrum"
elseif (strsearch(datasets, "ScientaEnergyDistribution", 0) >= 0)
datasetname = "ScientaEnergyDistribution"
elseif (strsearch(datasets, "ImageEnergyDistribution", 0) >= 0)
datasetname = "ImageEnergyDistribution"
elseif (strsearch(datasets, "Counts", 0) >= 0)
datasetname = "Counts"
elseif (strsearch(datasets, "SampleCurrent", 0) >= 0)
datasetname = "SampleCurrent"
variable nds = ItemsInList(datasets)
variable ids
string sds
variable np = ItemsInList(pref_datasets)
variable ip
string sp
variable found = 0
if (nds > 0)
for (ip = 0; ip < np; ip += 1)
for (ids = 0; ids < nds; ids += 1)
sds = StringFromList(ids, datasets)
index = ItemsInList(sds, "/") - 1
sds = StringFromList(index, sds, "/")
sp = StringFromList(ip, pref_datasets)
if (StringMatch(sds, sp))
found = 1
break
endif
endfor
if (found)
break
endif
endfor
if (!found)
ids = 0
sds = StringFromList(ids, datasets)
index = ItemsInList(sds, "/") - 1
sds = StringFromList(index, sds, "/")
endif
else
datasetname = StringFromList(0, datasets)
index = ItemsInList(datasetname, "/") - 1
datasetname = StringFromList(index, datasetname, "/")
endif
if (strlen(datasetname) == 0)
return ""
endif
string datasetpath
string datasetname = sds
datasetpath = scanpath + "/" + datasetname
datasetpath = ReplaceString("//", datasetpath, "/")
STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf.
@ -673,7 +750,7 @@ function /s psh5_load_scan_preview(fileID, scanpath, [set_scale])
endif
string dataname
if (di.ndims < 3)
if (di.ndims < 2)
HDF5LoadData /O /Q /Z fileID, datasetpath
dataname = StringFromList(0, S_waveNames)
wave /z data = $dataname
@ -803,6 +880,9 @@ end
///
/// @return name of loaded wave if successful. empty string otherwise.
///
/// @todo images are transposed in the first two dimensions.
/// this is useful for Scienta images but may not be appropriate for other sources.
///
function /s psh5_load_dataset_slabs(fileID, datapath, datasetname, [progress])
variable fileID
string datapath
@ -927,6 +1007,9 @@ end
///
/// @return name of loaded wave if successful. empty string otherwise.
///
/// @todo images are transposed in the first two dimensions.
/// this is useful for Scienta images but may not be appropriate for other data sources.
///
function /s psh5_load_dataset_slab(fileID, datapath, datasetname, dim2start, dim2count, dim3start, dim3count)
variable fileID
string datapath
@ -1010,42 +1093,63 @@ end
///
/// dimension labels are required by scaling functions.
///
/// @param data data wave as loaded from PShell file
///
/// @return @arg 0 all labels set successfully.
/// @arg 1 unidentified data source.
/// @arg 2 wave does not contain data.
///
function ps_set_dimlabels(data)
wave data
string name = NameOfWave(data)
// intrinsic dimensions
strswitch(name)
case "ScientaImage":
setdimlabel 0, -1, $kEnergyDimLabel, data
setdimlabel 1, -1, $kAngleDimLabel, data
if (WaveDims(data) >= 3)
setdimlabel 2, -1, $kScanDimLabel, data
endif
break
case "ImageAngleDistribution":
case "ScientaAngleDistribution":
if (WaveDims(data) >= 2)
setdimlabel 0, -1, $kScanDimLabel, data
setdimlabel 1, -1, $kAngleDimLabel, data
else
setdimlabel 0, -1, $kAngleDimLabel, data
endif
break
case "ScientaSpectrum":
case "ImageEnergyDistribution":
case "ScientaEnergyDistribution":
if (WaveDims(data) >= 2)
setdimlabel 0, -1, $kScanDimLabel, data
setdimlabel 1, -1, $kEnergyDimLabel, data
else
variable dummy
try
// intrinsic dimensions
strswitch(name)
case "ScientaImage":
setdimlabel 0, -1, $kEnergyDimLabel, data
endif
break
default:
setdimlabel 0, -1, $kScanDimLabel, data
endswitch
setdimlabel 1, -1, $kAngleDimLabel, data
if (WaveDims(data) >= 3)
setdimlabel 2, -1, $kScanDimLabel, data
endif
AbortOnRTE
break
case "ImageAngleDistribution":
case "ScientaAngleDistribution":
if (WaveDims(data) >= 2)
setdimlabel 0, -1, $kScanDimLabel, data
setdimlabel 1, -1, $kAngleDimLabel, data
else
setdimlabel 0, -1, $kAngleDimLabel, data
endif
AbortOnRTE
break
case "ScientaSpectrum":
case "ImageEnergyDistribution":
case "ScientaEnergyDistribution":
if (WaveDims(data) >= 2)
setdimlabel 0, -1, $kScanDimLabel, data
setdimlabel 1, -1, $kEnergyDimLabel, data
else
setdimlabel 0, -1, $kEnergyDimLabel, data
endif
AbortOnRTE
break
default:
if (WaveDims(data) == 1)
setdimlabel 0, -1, $kScanDimLabel, data
AbortOnRTE
else
return 1
endif
endswitch
catch
dummy = GetRTError(1)
return 2
endtry
return 0
end
/// set the dimension scales of loaded PShell Scienta datasets according to attributes.
@ -1219,7 +1323,7 @@ function ps_detect_scale(ax, lo, hi, un)
if (!WaveExists(scanner))
wave /z /SDFR=attrDF scanner = $ScanWritables[0]
endif
if (WaveExists(scanner))
if (WaveExists(scanner) && (numpnts(scanner) >= 1))
lo[%$kScanDimLabel] = scanner[0]
hi[%$kScanDimLabel] = scanner[numpnts(scanner)-1]
ax[%$kScanDimLabel] = NameOfWave(scanner)
@ -1362,7 +1466,9 @@ function /s psh5_load_reduced(ANickName, APathName, AFileName, reduction_func, r
string folder
sg = StringFromList(ig, s_scanpaths)
folder = CleanupName(ReplaceString("/", sg, ""), 0)
folder = ReplaceString("/", sg, "")
folder = ReplaceString(" ", folder, "")
folder = CleanupName(folder, 0)
setdatafolder fileDF
newdatafolder /s /o $folder
dfref dataDF = GetDataFolderDFR()