updates: pshell import, angle-scans, elog
- pshell import: fix units and data scaling. - pshell import: support new multi-region scans. - angle scans: add trim function. - angle scans: update import_tpi_scan function. - angle scans: fix scales of check waves in normalization. - area display: new cursor mode for background selection. - elog: bugfixes (attachment list, check existing logbook).
This commit is contained in:
parent
9a65d26984
commit
80a01f2bdb
@ -300,6 +300,7 @@ function normalize_strip_theta(strip, theta, [theta_offset, smooth_method, smoot
|
||||
duplicate /free dist, dist_smoo
|
||||
duplicate /free theta, theta_int
|
||||
theta_int = theta - theta_offset
|
||||
setscale /p x theta_int[0], theta_int[1] - theta_int[0], waveunits(theta,-1), dist, dist_smoo
|
||||
variable nx = dimsize(strip, 0)
|
||||
variable ix
|
||||
|
||||
@ -336,6 +337,7 @@ function normalize_strip_theta(strip, theta, [theta_offset, smooth_method, smoot
|
||||
if (check)
|
||||
duplicate /o dist, check_dist
|
||||
duplicate /o dist_smoo, check_smoo
|
||||
setscale /p x dimoffset(dist,0), dimdelta(dist,0), waveunits(dist,0), check_dist, check_smoo
|
||||
endif
|
||||
end
|
||||
|
||||
@ -1861,7 +1863,7 @@ function /s display_scanlines(nickname, alpha_lo, alpha_hi, m_theta, m_tilt, m_p
|
||||
make /n=1 /d /free d_polar, d_azi
|
||||
variable n_alpha = round(alpha_hi - alpha_lo) + 1
|
||||
make /n=(n_alpha) /d /free analyser
|
||||
setscale /i x alpha_lo, alpha_hi, "deg", analyser
|
||||
setscale /i x alpha_lo, alpha_hi, "°", analyser
|
||||
analyser = x
|
||||
|
||||
convert_angles_ttpa2polar(m_theta, loc_m_tilt, m_phi, analyser, d_polar, d_azi)
|
||||
@ -2586,8 +2588,35 @@ end
|
||||
|
||||
/// import a hemispherical scan from theta-phi-intensity waves and display it
|
||||
///
|
||||
/// @warning EXPERIMENTAL
|
||||
/// the interface and behaviour of this function may change
|
||||
/// in the tpi format, the hemi scan data is represented
|
||||
/// by a triple of flat one-dimensional waves
|
||||
/// corresponding to the polar angle (theta), azimuthal angle (phi) and intensity.
|
||||
/// no specific sort order is required.
|
||||
///
|
||||
/// @param nickname nick name for output data
|
||||
/// @arg in default mode, this will become the name of a child folder containing the output.
|
||||
/// @arg in XPDplot mode, this will become a prefix of the generated data in the root folder.
|
||||
///
|
||||
/// @param theta theta angles, 0 = normal emission.
|
||||
///
|
||||
/// @param phi phi angles, 0 = azimuthal origin. size = dimsize(data, 1)
|
||||
///
|
||||
/// @param intensity intensity wave, see requirements above.
|
||||
///
|
||||
/// @param npolar number of polar angles, determines polar and azimuthal step size.
|
||||
/// default = 91 (1 degree steps)
|
||||
///
|
||||
/// @param folding rotational averaging.
|
||||
/// example: 3 = average to 3-fold symmetry.
|
||||
/// default = 1.
|
||||
///
|
||||
/// @param nograph display a new graph window?
|
||||
/// @arg 0 (default) display a new polar graph
|
||||
/// @arg 1 don't display a new graph
|
||||
///
|
||||
/// @param xpdplot XPDplot compatibility
|
||||
/// @arg 0 (default) create waves in child folder $nickname
|
||||
/// @arg 1 create waves in root folder (compatible with XPDplot)
|
||||
///
|
||||
function import_tpi_scan(nickname, theta, phi, intensity, [folding, npolar, nograph, xpdplot])
|
||||
string nickname
|
||||
@ -2622,7 +2651,43 @@ function import_tpi_scan(nickname, theta, phi, intensity, [folding, npolar, nogr
|
||||
fold_phi = fold_phi >= 180 ? fold_phi + 360 / folding - fold_phi : fold_phi + 360 / folding
|
||||
endfor
|
||||
|
||||
display_hemi_scan(nickname)
|
||||
if (nograph==0)
|
||||
display_hemi_scan(nickname)
|
||||
endif
|
||||
end
|
||||
|
||||
/// trim a hemispherical scan at grazing angle
|
||||
///
|
||||
/// the function recalaculates the values wave from totals and weights
|
||||
/// but sets elements above a given polar angle to nan.
|
||||
///
|
||||
/// @param nickname name of the scan dataset.
|
||||
/// can be empty if no prefix is used.
|
||||
/// the dataset must be in the current datafolder.
|
||||
///
|
||||
/// @param theta_max highest polar angle to keep (0...90 degrees).
|
||||
///
|
||||
function trim_hemi_scan(nickname, theta_max)
|
||||
string nickname
|
||||
variable theta_max
|
||||
|
||||
if (strlen(nickname))
|
||||
string s_prefix = nickname + "_"
|
||||
string s_int = s_prefix + "i"
|
||||
else
|
||||
s_prefix = ""
|
||||
s_int = "values"
|
||||
endif
|
||||
string s_totals = s_prefix + "tot"
|
||||
string s_weights = s_prefix + "wt"
|
||||
string s_polar = s_prefix + "pol"
|
||||
|
||||
wave w_polar = $s_polar
|
||||
wave w_values = $s_int
|
||||
wave w_totals = $s_totals
|
||||
wave w_weights = $s_weights
|
||||
|
||||
w_values = w_polar <= theta_max ? w_totals / w_weights : nan
|
||||
end
|
||||
|
||||
/// extract a polar cut from a hemispherical scan.
|
||||
@ -2772,7 +2837,7 @@ function /wave hemi_azi_cut(nickname, pol)
|
||||
make /n=(nsel) /o $s_cut
|
||||
wave w_cut = $s_cut
|
||||
w_cut = w_values[sel]
|
||||
setscale /i x w_azim[sel[0]], w_azim[sel[nsel-1]], "deg", w_cut
|
||||
setscale /i x w_azim[sel[0]], w_azim[sel[nsel-1]], "°", w_cut
|
||||
return w_cut
|
||||
else
|
||||
return $""
|
||||
|
||||
@ -436,7 +436,7 @@ static function setup_detector()
|
||||
setdatafolder $(package_path)
|
||||
|
||||
make /n=31 /o detector_angle, detector_pol, detector_az, detector_rad
|
||||
setscale /i x -30, 30, "deg", detector_angle, detector_pol, detector_az, detector_rad
|
||||
setscale /i x -30, 30, "°", detector_angle, detector_pol, detector_az, detector_rad
|
||||
detector_angle = x
|
||||
|
||||
setdatafolder saveDF
|
||||
@ -573,7 +573,7 @@ static function update_detector(theta, tilt, phi, range)
|
||||
//m_phi *= -1 // checked 140702
|
||||
|
||||
wave detector_angle, detector_pol, detector_az, detector_rad
|
||||
setscale /i x -range/2, +range/2, "deg", detector_angle
|
||||
setscale /i x -range/2, +range/2, "°", detector_angle
|
||||
detector_angle = x
|
||||
|
||||
convert_angles_ttpa2polar(m_theta, m_tilt, m_phi, detector_angle, detector_pol, detector_az)
|
||||
|
||||
@ -196,6 +196,7 @@ function /s ad_display_profiles(image, [filter])
|
||||
view_filter_options = ""
|
||||
variable /g view_filter_smoothing_x = 1
|
||||
variable /g view_filter_smoothing_y = 1
|
||||
variable /g view_cursor_mode = 0
|
||||
string dfname = ReplaceString("root:", GetDataFolder(1, imagedf), "")
|
||||
string graphtitle = dfname + NameOfWave(image) + " Profiles"
|
||||
string /g prof_graphname = graphname_from_dfref(imagedf, "prof_")
|
||||
@ -348,15 +349,88 @@ function ad_update_profiles(image)
|
||||
return 0
|
||||
end
|
||||
|
||||
/// switch cursors on a profiles graph
|
||||
///
|
||||
/// the standard cursors allow to select the profiles to display in the profiles panes.
|
||||
/// additional cursors are shown in the profiles panes.
|
||||
///
|
||||
/// in the background selection mode, additional cursors allow the user to select
|
||||
/// the limits of the background and peak integration regions.
|
||||
/// the meaning of the cursors depends on the particular processing function.
|
||||
///
|
||||
/// @param mode cursor mode.
|
||||
/// @arg 0 (default) standard profile selection. cursors C-F on profile panes.
|
||||
/// @arg 1 background selection. cursors A-F on image.
|
||||
///
|
||||
/// @param image image displayed in the graph.
|
||||
/// this is the original image, not the one in the view data folder.
|
||||
///
|
||||
function ad_profiles_cursor_mode(image, mode)
|
||||
wave image
|
||||
variable mode
|
||||
|
||||
dfref savedf = GetDataFolderDFR()
|
||||
wave view_image = get_view_image(image)
|
||||
dfref viewdf = GetWavesDataFolderDFR(view_image)
|
||||
svar /sdfr=viewdf graphname = prof_graphname
|
||||
nvar /sdfr=viewdf cursor_mode = view_cursor_mode
|
||||
wave /sdfr=viewdf xprofiles, yprofiles
|
||||
|
||||
variable dx = DimSize(view_image, 0)
|
||||
variable dy = DimSize(view_image, 1)
|
||||
switch(mode)
|
||||
case 1: // background selection
|
||||
Cursor /w=$graphname /A=0 /P /I /S=2 /H=1 /L=1 A view_image 0, 0
|
||||
Cursor /w=$graphname /A=0 /P /I /S=2 /H=1 /L=1 B view_image dx-1, dy-1
|
||||
Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 C view_image round(0.2 * dx) -1, 0
|
||||
Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 D view_image round(0.8 * dx) -1, 0
|
||||
Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 E view_image round(0.4 * dx) -1, 0
|
||||
Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 F view_image round(0.6 * dx) -1, 0
|
||||
|
||||
ShowInfo /w=$graphname /CP=0
|
||||
cursor_mode = mode
|
||||
break
|
||||
default:
|
||||
Cursor /w=$graphname /A=1 /P /I /S=2 /H=1 /L=1 A view_image 0,0
|
||||
Cursor /w=$graphname /A=1 /P /I /S=2 /H=1 /L=1 B view_image dx-1, dy-1
|
||||
variable pcurs
|
||||
pcurs = floor(DimSize(xprofiles, 0) / 3)
|
||||
Cursor /w=$graphname /A=0 /P /S=1 /H=0 C xprofiles#2 pcurs
|
||||
pcurs = floor(DimSize(xprofiles, 0) * 2 / 3)
|
||||
Cursor /w=$graphname /A=0 /P /S=1 /H=0 D xprofiles#2 pcurs
|
||||
pcurs = floor(DimSize(yprofiles, 0) / 3)
|
||||
Cursor /w=$graphname /A=0 /P /S=1 /H=0 E yprofiles#2 pcurs
|
||||
pcurs = floor(DimSize(yprofiles, 0) * 2 / 3)
|
||||
Cursor /w=$graphname /A=0 /P /S=1 /H=0 F yprofiles#2 pcurs
|
||||
ShowInfo /w=$graphname /CP=0
|
||||
cursor_mode = 0
|
||||
endswitch
|
||||
|
||||
setdatafolder savedf
|
||||
return 0
|
||||
end
|
||||
|
||||
/// move a cursor to the specified position in a profiles graph.
|
||||
///
|
||||
/// this function can only set cursors in the image part of the profiles graph.
|
||||
///
|
||||
/// @param image image displayed in the graph.
|
||||
/// this is the original image, not the one in the view data folder.
|
||||
/// @param cursorname name of the cursor, e.g. "A" or "B".
|
||||
/// other cursors are allowed but need to be activated separately.
|
||||
/// @param xa x-coordinate to move the cursor to.
|
||||
/// the position is coerced to the image scale. +/-inf is allowed.
|
||||
/// @param ya y-coordinate to move the cursor to.
|
||||
/// the position is coerced to the image scale. +/-inf is allowed.
|
||||
/// @param pscale scaling of the position argument
|
||||
/// @arg 0 (default) wave scaling
|
||||
/// @arg 1 point scaling
|
||||
///
|
||||
function ad_profiles_set_cursor(image, cursorname, xa, ya, [pscale])
|
||||
wave image // image displayed in the graph. this is the original image, not the one in the view data folder.
|
||||
string cursorname // name of the cursor. must be "A" or "B".
|
||||
variable xa, ya // position to move the cursor to.
|
||||
// the position is coerced to the image scale. +/-inf is allowed.
|
||||
variable pscale // scaling of the position argument
|
||||
// 0 (default) = wave scaling
|
||||
// 1 = point scaling
|
||||
wave image
|
||||
string cursorname
|
||||
variable xa, ya
|
||||
variable pscale
|
||||
|
||||
if (ParamIsDefault(pscale))
|
||||
pscale = 0
|
||||
|
||||
@ -1667,12 +1667,12 @@ function adh5_scale_scienta(data)
|
||||
case 1: // Angular45
|
||||
ALow = -45/2
|
||||
AHigh = +45/2
|
||||
AUnit = "deg"
|
||||
AUnit = "°"
|
||||
break
|
||||
case 2: // Angular60
|
||||
ALow = -60/2
|
||||
AHigh = +60/2
|
||||
AUnit = "deg"
|
||||
AUnit = "°"
|
||||
break
|
||||
endswitch
|
||||
endif
|
||||
|
||||
@ -1090,6 +1090,7 @@ static function /df load_pshell_file(filename, [options])
|
||||
string reduction_params = pref_params
|
||||
if (prompt_func_params(reduction_func, reduction_params) == 0)
|
||||
pref_params = reduction_params
|
||||
print reduction_func, reduction_params
|
||||
psh5_load_reduced(nickname, "pearl_explorer_filepath", filename, $reduction_func, reduction_params)
|
||||
svar s_filepath
|
||||
loaded_filename = s_filepath
|
||||
@ -1141,6 +1142,7 @@ static function /df load_hdf_file(filename, [options])
|
||||
string reduction_params = pref_params
|
||||
if (prompt_func_params(reduction_func, reduction_params) == 0)
|
||||
pref_params = reduction_params
|
||||
print reduction_func, reduction_params
|
||||
loaded_filename = adh5_load_reduced(nickname, "pearl_explorer_filepath", filename, $reduction_func, reduction_params)
|
||||
endif
|
||||
break
|
||||
|
||||
@ -426,6 +426,13 @@ function elog_create_logbook(name, [template])
|
||||
dfref df_volatile_root = get_elog_df("", kdfVolatile)
|
||||
dfref df_volatile_parent = df_volatile_root:logbooks
|
||||
|
||||
setdatafolder df_persistent_parent
|
||||
if (CheckName(name, 11) != 0)
|
||||
setdatafolder savedf
|
||||
Abort "invalid logbook name"
|
||||
return -1
|
||||
endif
|
||||
|
||||
if (strlen(template) > 0)
|
||||
dfref df_template = get_elog_df(template, kdfTemplates)
|
||||
dfref df_existing = get_elog_df(name, kdfPersistent)
|
||||
@ -1380,13 +1387,14 @@ static function update_attach_items(logbook)
|
||||
FindValue /text=s /txop=4 /z attach_list
|
||||
if (v_value < 0)
|
||||
k = DimSize(attach_list, 0)
|
||||
InsertPoints /M=0 k, 1, attach_list, attach_sel
|
||||
attach_list[i][kAttachColSel] = ""
|
||||
attach_list[i][kAttachColTitle] = ""
|
||||
Redimension /n=(k+1,3) attach_list, attach_sel
|
||||
//InsertPoints /M=0 k, 1, attach_list, attach_sel
|
||||
attach_list[k][kAttachColSel] = ""
|
||||
attach_list[k][kAttachColTitle] = ""
|
||||
attach_list[k][kAttachColName] = s
|
||||
attach_sel[i][kAttachColSel] = 32
|
||||
attach_sel[i][kAttachColTitle] = 0
|
||||
attach_sel[i][kAttachColName] = 0
|
||||
attach_sel[k][kAttachColSel] = 32
|
||||
attach_sel[k][kAttachColTitle] = 0
|
||||
attach_sel[k][kAttachColName] = 0
|
||||
endif
|
||||
endfor
|
||||
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.36
|
||||
#pragma ModuleName = PearlPShellImport
|
||||
#pragma version = 1.02
|
||||
#pragma version = 1.03
|
||||
#include <HDF5 Browser>
|
||||
#include "pearl-gui-tools"
|
||||
#include "pearl-area-import"
|
||||
@ -309,6 +309,15 @@ function /s psh5_load_preview(ANickName, APathName, AFileName, [load_data, load_
|
||||
ig = 0
|
||||
endif
|
||||
sg = StringFromList(ig, scanpaths)
|
||||
|
||||
if (load_attr)
|
||||
setdatafolder fileDF
|
||||
newdatafolder /o/s attr
|
||||
killwaves /a/z
|
||||
psh5_load_scan_attrs(fileID, sg)
|
||||
endif
|
||||
|
||||
setdatafolder fileDF
|
||||
dataname = psh5_load_scan_preview(fileID, sg, set_scale=load_attr, pref_datasets=pref_datasets)
|
||||
|
||||
wave /z data = $dataname
|
||||
@ -320,13 +329,6 @@ function /s psh5_load_preview(ANickName, APathName, AFileName, [load_data, load_
|
||||
print "no data found in file " + AFileName
|
||||
endif
|
||||
|
||||
if (load_attr)
|
||||
setdatafolder saveDF
|
||||
newdatafolder /o/s attr
|
||||
killwaves /a/z
|
||||
psh5_load_scan_attrs(fileID, sg)
|
||||
setdatafolder ::
|
||||
endif
|
||||
else
|
||||
print "no scans found in file " + AFileName
|
||||
endif
|
||||
@ -346,6 +348,7 @@ end
|
||||
///
|
||||
/// data is loaded into the current data folder.
|
||||
/// attribute datasets are loaded into sub-folder `attr`.
|
||||
/// region datasets are loaded into region sub-folders.
|
||||
/// existing data, if present, is overwritten.
|
||||
///
|
||||
/// @param fileID ID of open HDF5 file from psh5_open_file().
|
||||
@ -382,13 +385,14 @@ function /s psh5_load_scan_complete(fileID, scanpath, [load_data, load_attr])
|
||||
string wavenames
|
||||
string attrnames
|
||||
psh5_load_scan_meta(fileID, scanpath)
|
||||
if (load_data)
|
||||
wavenames = psh5_load_scan_data(fileID, scanpath)
|
||||
endif
|
||||
if (load_attr)
|
||||
newdatafolder /s /o attr
|
||||
attrnames = psh5_load_scan_attrs(fileID, scanpath)
|
||||
endif
|
||||
if (load_data)
|
||||
setdatafolder dataDF
|
||||
wavenames = psh5_load_scan_data(fileID, scanpath)
|
||||
endif
|
||||
if (load_data && load_attr)
|
||||
setdatafolder dataDF
|
||||
ps_scale_datasets()
|
||||
@ -439,18 +443,72 @@ end
|
||||
///
|
||||
/// @return semicolon-separated list of dataset paths.
|
||||
///
|
||||
function /s psh5_list_scan_datasets(fileID, scanpath)
|
||||
/// @version since version 1.03 this function returns paths relative to scanpath.
|
||||
///
|
||||
function /s psh5_list_scan_datasets(fileID, scanpath, [include_regions])
|
||||
variable fileID
|
||||
string scanpath
|
||||
variable include_regions
|
||||
|
||||
if (ParamIsDefault(include_regions))
|
||||
include_regions = 0
|
||||
endif
|
||||
string result
|
||||
|
||||
HDF5ListGroup /TYPE=2 /Z fileID, scanpath
|
||||
result = S_HDF5ListGroup
|
||||
|
||||
if (include_regions)
|
||||
HDF5ListGroup /R /TYPE=2 /Z fileID, scanpath
|
||||
variable n = ItemsInList(S_HDF5ListGroup)
|
||||
variable i
|
||||
string ds
|
||||
string region_datasets
|
||||
for (i = 0; i < n; i += 1)
|
||||
ds = StringFromList(i, S_HDF5ListGroup)
|
||||
if (StringMatch(ds, "region*/*"))
|
||||
//region_datasets = psh5_list_scan_datasets(fileID, ReplaceString("//", scanpath + "/" + region, "/"), include_regions=0)
|
||||
result = AddListItem(ds, result, ";", inf)
|
||||
endif
|
||||
endfor
|
||||
endif
|
||||
|
||||
return result
|
||||
end
|
||||
|
||||
/// list regions of a PShell scan group.
|
||||
///
|
||||
/// the function returns a list of all region groups of the selected scan.
|
||||
///
|
||||
/// @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".
|
||||
///
|
||||
/// @return semicolon-separated list of datagroup paths.
|
||||
///
|
||||
function /s psh5_list_scan_regions(fileID, scanpath)
|
||||
variable fileID
|
||||
string scanpath
|
||||
|
||||
HDF5ListGroup /F /TYPE=2 /Z fileID, scanpath
|
||||
HDF5ListGroup /TYPE=1 /Z fileID, scanpath
|
||||
variable n = ItemsInList(S_HDF5ListGroup)
|
||||
variable i
|
||||
string result = ""
|
||||
string s
|
||||
for (i = 0; i < n; i += 1)
|
||||
s = StringFromList(i, S_HDF5ListGroup)
|
||||
if (StringMatch(s, "region*"))
|
||||
result = AddListItem(s, result, ";", inf)
|
||||
endif
|
||||
endfor
|
||||
|
||||
return S_HDF5ListGroup
|
||||
return result
|
||||
end
|
||||
|
||||
/// load all datasets of a PShell scan group.
|
||||
///
|
||||
/// data is loaded into the current data folder.
|
||||
/// region datasets are loaded into the respective region sub-folders.
|
||||
///
|
||||
/// this function does not scale the datasets.
|
||||
/// call ps_scale_datasets() separately.
|
||||
@ -464,22 +522,18 @@ end
|
||||
function /s psh5_load_scan_data(fileID, scanpath)
|
||||
variable fileID
|
||||
string scanpath
|
||||
|
||||
string datasets = psh5_list_scan_datasets(fileID, scanpath, include_regions=1)
|
||||
variable nds = ItemsInList(datasets)
|
||||
variable ids
|
||||
string sds
|
||||
string sw
|
||||
string wavenames = ""
|
||||
|
||||
HDF5ListGroup /F /TYPE=2 /Z fileID, scanpath
|
||||
|
||||
if (!v_flag)
|
||||
variable ids
|
||||
variable nds = ItemsInList(S_HDF5ListGroup, ";")
|
||||
string sds
|
||||
string sw
|
||||
|
||||
for (ids = 0; ids < nds; ids += 1)
|
||||
sds = StringFromList(ids, S_HDF5ListGroup, ";")
|
||||
sw = psh5_load_dataset(fileID, "", sds, set_scale=0)
|
||||
wavenames = AddListItem(sw, wavenames, ";", inf)
|
||||
endfor
|
||||
endif
|
||||
for (ids = 0; ids < nds; ids += 1)
|
||||
sds = StringFromList(ids, datasets)
|
||||
sw = psh5_load_dataset(fileID, scanpath, sds, set_scale=0)
|
||||
wavenames = AddListItem(sw, wavenames, ";", inf)
|
||||
endfor
|
||||
|
||||
return wavenames
|
||||
end
|
||||
@ -617,12 +671,18 @@ end
|
||||
/// - wave scaling is set if the necessary scan attributes have been loaded and the `set_scale` option is selected (default).
|
||||
/// the attributes must be loaded by psh5_load_scan_meta() and psh5_load_scan_attrs() (attr_sets=2).
|
||||
///
|
||||
/// the dataset is loaded into the current data folder unless datasetname contains a region specifier.
|
||||
/// in the latter case, the dataset is loaded into sub-folder with the name of the region.
|
||||
/// the function returns from the original data folder.
|
||||
///
|
||||
/// @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".
|
||||
///
|
||||
/// @param dataset name of the dataset.
|
||||
/// @param datasetname name of the dataset.
|
||||
/// the name of the loaded wave is a cleaned up version of the dataset name.
|
||||
/// the name can include the region name as a relative path, e.g. "region1/ScientaSpectrum".
|
||||
/// in this case, the dataset is loaded into a sub-folder named "region1".
|
||||
///
|
||||
/// @param set_scale by default, the function tries to set the wave scaling if the attributes have been loaded.
|
||||
/// if multiple datasets are loaded from a file,
|
||||
@ -632,6 +692,8 @@ end
|
||||
///
|
||||
/// @return name of loaded wave if successful. empty string otherwise.
|
||||
///
|
||||
/// @version this function supports regions as of version 1.03.
|
||||
///
|
||||
function /s psh5_load_dataset(fileID, scanpath, datasetname, [set_scale])
|
||||
variable fileID
|
||||
string scanpath
|
||||
@ -642,10 +704,24 @@ function /s psh5_load_dataset(fileID, scanpath, datasetname, [set_scale])
|
||||
set_scale = 1
|
||||
endif
|
||||
|
||||
dfref base_df = GetDataFolderDFR()
|
||||
|
||||
string datasetpath
|
||||
datasetpath = scanpath + "/" + datasetname
|
||||
datasetpath = ReplaceString("//", datasetpath, "/")
|
||||
|
||||
string regionname
|
||||
string regionpath
|
||||
if (ItemsInList(datasetname, "/") >= 2)
|
||||
regionname = StringFromList(0, datasetname, "/")
|
||||
regionpath = ReplaceString("//", scanpath + "/" + regionname, "/")
|
||||
datasetname = RemoveListItem(0, datasetname, "/")
|
||||
NewDataFolder /o/s $regionname
|
||||
else
|
||||
regionname = ""
|
||||
regionpath = scanpath
|
||||
endif
|
||||
|
||||
STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf.
|
||||
InitHDF5DataInfo(di)
|
||||
variable err = HDF5DatasetInfo(fileID, datasetpath, 0, di)
|
||||
@ -659,12 +735,12 @@ function /s psh5_load_dataset(fileID, scanpath, datasetname, [set_scale])
|
||||
HDF5LoadData /O /Q /Z fileID, datasetpath
|
||||
dataname = StringFromList(0, S_waveNames)
|
||||
else
|
||||
dataname = psh5_load_dataset_slabs(fileID, scanpath, datasetname)
|
||||
dataname = psh5_load_dataset_slabs(fileID, regionpath, datasetname)
|
||||
endif
|
||||
|
||||
wave /z data = $dataname
|
||||
if (waveexists(data))
|
||||
psh5_load_dataset_meta(fileID, scanpath, datasetname, data)
|
||||
psh5_load_dataset_meta(fileID, regionpath, datasetname, data)
|
||||
ps_set_dimlabels(data)
|
||||
if (set_scale)
|
||||
ps_scale_dataset(data)
|
||||
@ -673,19 +749,22 @@ function /s psh5_load_dataset(fileID, scanpath, datasetname, [set_scale])
|
||||
dataname = ""
|
||||
endif
|
||||
|
||||
setdatafolder base_df
|
||||
return dataname
|
||||
end
|
||||
|
||||
/// select the preferred dataset from a list of available datasets.
|
||||
///
|
||||
/// @param file_datasets semicolon-separated list of datasets that are available in the file.
|
||||
/// the items may include a path separated by slashes "/".
|
||||
/// only the last component of the path is checked.
|
||||
///
|
||||
/// @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 file dataset is selected.
|
||||
///
|
||||
/// @return name of selected dataset.
|
||||
/// @return selected dataset.
|
||||
///
|
||||
static function /s select_dataset(file_datasets, pref_datasets)
|
||||
string file_datasets
|
||||
@ -695,6 +774,7 @@ static function /s select_dataset(file_datasets, pref_datasets)
|
||||
variable nds = ItemsInList(file_datasets)
|
||||
variable ids
|
||||
string sds = ""
|
||||
string mds = ""
|
||||
variable np = ItemsInList(pref_datasets)
|
||||
variable ip
|
||||
string sp
|
||||
@ -704,9 +784,9 @@ static function /s select_dataset(file_datasets, pref_datasets)
|
||||
for (ids = 0; ids < nds; ids += 1)
|
||||
sds = StringFromList(ids, file_datasets)
|
||||
index = ItemsInList(sds, "/") - 1
|
||||
sds = StringFromList(index, sds, "/")
|
||||
mds = StringFromList(index, sds, "/")
|
||||
sp = StringFromList(ip, pref_datasets)
|
||||
if (StringMatch(sds, sp))
|
||||
if (StringMatch(mds, sp))
|
||||
found = 1
|
||||
break
|
||||
endif
|
||||
@ -718,8 +798,6 @@ static function /s select_dataset(file_datasets, pref_datasets)
|
||||
if (!found)
|
||||
ids = 0
|
||||
sds = StringFromList(ids, file_datasets)
|
||||
index = ItemsInList(sds, "/") - 1
|
||||
sds = StringFromList(index, sds, "/")
|
||||
endif
|
||||
endif
|
||||
|
||||
@ -766,7 +844,7 @@ function /s psh5_load_scan_preview(fileID, scanpath, [set_scale, pref_datasets])
|
||||
dfref saveDF = GetDataFolderDFR()
|
||||
dfref dataDF = saveDF
|
||||
|
||||
string datasets = psh5_list_scan_datasets(fileID, scanpath)
|
||||
string datasets = psh5_list_scan_datasets(fileID, scanpath, include_regions=1)
|
||||
string datasetname = select_dataset(datasets, pref_datasets)
|
||||
string datasetpath
|
||||
datasetpath = scanpath + "/" + datasetname
|
||||
@ -995,7 +1073,8 @@ end
|
||||
/// @param datapath path to the containing group in the HDF5 file.
|
||||
/// path separator is the slash "/".
|
||||
///
|
||||
/// @param dataset name of the dataset.
|
||||
/// @param datasetname name of the dataset.
|
||||
/// may include relative path.
|
||||
///
|
||||
/// @param datawave metadata is added to the wave note of this wave.
|
||||
///
|
||||
@ -1364,42 +1443,92 @@ function ps_set_dimlabels2(data, name)
|
||||
return 0
|
||||
end
|
||||
|
||||
/// find the scan folder
|
||||
///
|
||||
/// the scan folder is the one that contains the :attr folder
|
||||
/// the data and scan folders may refer to the same folder.
|
||||
///
|
||||
static function /df find_scan_folder(dataDF)
|
||||
dfref dataDF
|
||||
|
||||
dfref attrDF = dataDF:attr
|
||||
if (!DataFolderRefStatus(attrDF))
|
||||
string df = GetDataFolder(1, dataDF) + ":"
|
||||
dfref scanDF = $df
|
||||
else
|
||||
dfref scanDF = dataDF
|
||||
endif
|
||||
return scanDF
|
||||
end
|
||||
|
||||
/// find the attributes data folder
|
||||
///
|
||||
/// this is the :attr folder.
|
||||
///
|
||||
static function /df find_attr_folder(dataDF)
|
||||
dfref dataDF
|
||||
|
||||
dfref attrDF = dataDF:attr
|
||||
if (!DataFolderRefStatus(attrDF))
|
||||
string df = GetDataFolder(1, dataDF) + ":"
|
||||
dfref scanDF = $df
|
||||
dfref attrDF = scanDF:attr
|
||||
endif
|
||||
return attrDF
|
||||
end
|
||||
|
||||
/// set the dimension scales of loaded PShell Scienta datasets according to attributes.
|
||||
///
|
||||
/// the datasets must be in the current data folder.
|
||||
/// all datasets listed in the ScanReadables waves are scaled
|
||||
/// according to the attribute waves in the :attr folder.
|
||||
/// datasets listed in the ScanReadables waves are scaled
|
||||
/// according to the attribute waves in the data, scan, and attributes folders,
|
||||
/// whichever is found first.
|
||||
///
|
||||
/// the dimension labels of the dataset waves must be set correctly, e.g. by ps_set_dimlabels().
|
||||
/// the current datafolder must contain the ScanReadables wave and the :attr folder.
|
||||
/// the ScanReadables text wave contains names of the waves to scale.
|
||||
/// wave names can include a relative path to a sub-folder. the path separator is "/".
|
||||
///
|
||||
/// the dimension labels of the dataset waves must have been set correctly, e.g. by ps_set_dimlabels().
|
||||
/// this is implicitly done by the high-level load functions.
|
||||
///
|
||||
/// @version this function supports regions from version 1.03.
|
||||
/// check that you're in the correct data folder!
|
||||
///
|
||||
function ps_scale_datasets()
|
||||
dfref dataDF = GetDataFolderDFR()
|
||||
dfref attrDF = :attr
|
||||
dfref scanDF = GetDataFolderDFR()
|
||||
dfref attrDF = find_attr_folder(scanDF)
|
||||
|
||||
make /n=3 /free lo, hi
|
||||
make /n=3 /t /free ax, un
|
||||
ps_detect_scale(ax, lo, hi, un)
|
||||
|
||||
wave /t /z /SDFR=dataDF ScanReadables
|
||||
wave /t /z /SDFR=scanDF ScanReadables
|
||||
if (WaveExists(ScanReadables))
|
||||
variable isr
|
||||
variable nsr = numpnts(ScanReadables)
|
||||
string ssr
|
||||
string sdf
|
||||
for (isr = 0; isr < nsr; isr += 1)
|
||||
wave /z /SDFR=dataDF wsr = $ScanReadables[isr]
|
||||
setdatafolder scanDF
|
||||
ssr = ScanReadables[isr]
|
||||
if (ItemsInList(ssr, "/") >= 2)
|
||||
sdf = StringFromList(0, ssr, "/")
|
||||
ssr = RemoveListItem(0, ssr, "/")
|
||||
setdatafolder $sdf
|
||||
endif
|
||||
wave /z wsr=$ssr
|
||||
if (WaveExists(wsr))
|
||||
ps_detect_scale(ax, lo, hi, un)
|
||||
ps_scale_dataset_2(wsr, ax, lo, hi, un)
|
||||
endif
|
||||
endfor
|
||||
endif
|
||||
setdatafolder scanDF
|
||||
end
|
||||
|
||||
/// set the dimension scales of a loaded PShell Scienta dataset according to attributes.
|
||||
///
|
||||
/// the attributes must be in the child folder `:attr` next to the dataset.
|
||||
/// the current datafolder must contain the :attr folder.
|
||||
/// the data wave can be in the current folder or a sub-folder.
|
||||
///
|
||||
/// the dimension labels of the dataset waves must be set correctly, cf. ps_set_dimlabels().
|
||||
/// the dimension labels of the dataset waves must have been set correctly, e.g. by ps_set_dimlabels().
|
||||
/// this is implicitly done by the high-level load functions.
|
||||
///
|
||||
/// the function is useful if a single dataset is loaded and scaled.
|
||||
@ -1408,27 +1537,48 @@ end
|
||||
/// @param data data wave to be scaled.
|
||||
/// dimension labels (index -1) must be set correctly, cf. ps_set_dimlabels().
|
||||
///
|
||||
/// @version this function supports regions from version 1.03.
|
||||
///
|
||||
function ps_scale_dataset(data)
|
||||
wave data
|
||||
|
||||
dfref saveDF = GetDataFolderDFR()
|
||||
dfref dataDF = GetWavesDataFolderDFR(data)
|
||||
setdatafolder dataDF
|
||||
|
||||
setdatafolder dataDF
|
||||
make /n=3 /free lo, hi
|
||||
make /n=3 /t /free ax, un
|
||||
ps_detect_scale(ax, lo, hi, un)
|
||||
ps_scale_dataset_2(data, ax, lo, hi, un)
|
||||
|
||||
setdatafolder saveDF
|
||||
end
|
||||
|
||||
static function /wave find_scale_wave(name, dataDF, scanDF, attrDF)
|
||||
string name
|
||||
dfref dataDF
|
||||
dfref scanDF
|
||||
dfref attrDF
|
||||
|
||||
wave /SDFR=dataDF /Z w = $name
|
||||
if (!WaveExists(w))
|
||||
wave /SDFR=scanDF /Z w = $name
|
||||
if (!WaveExists(w))
|
||||
wave /SDFR=attrDF /Z w = $name
|
||||
endif
|
||||
endif
|
||||
return w
|
||||
end
|
||||
|
||||
/// detect the dimension scales from attributes.
|
||||
///
|
||||
/// the function checks the current data folder and the sub-folder `:attr` for scan parameters.
|
||||
/// the function checks the data , scan and attributes folders for scan parameters.
|
||||
/// the results are written to the provided waves.
|
||||
/// the function is normally called by ps_scale_datasets() but can also be used independently.
|
||||
///
|
||||
/// the current datafolder must be the data or the scan folder.
|
||||
/// the data folder contains the waves that are to be scaled.
|
||||
/// the scan folder contains the scan positions and the :attr folder.
|
||||
///
|
||||
/// the provided waves are redimensioned by the function, and dimension labels are set.
|
||||
/// the scale parameters can then be extracted by keyword, e.g.,
|
||||
/// @arg `lo[%%energy]` analyser energy dimension.
|
||||
@ -1436,13 +1586,14 @@ end
|
||||
/// @arg `lo[%%scan]` scan dimension.
|
||||
/// @arg `lo[%%data]` data dimension.
|
||||
///
|
||||
/// the function tries to read the following waves,
|
||||
/// and may fall back to more or less reasonable default values if they are not found.
|
||||
/// @arg `:attr:LensMode`
|
||||
/// @arg `:attr:ScientaChannelBegin`
|
||||
/// @arg `:attr:ScientaChannelEnd`
|
||||
/// @arg `:attr:ScientaSliceBegin`
|
||||
/// @arg `:attr:ScientaSliceEnd`
|
||||
/// the function tries to read the following waves, in the data, scan, and attributes folders,
|
||||
/// where the first folder in the list takes precedence.
|
||||
/// it may fall back to more or less reasonable default values if no data is not found.
|
||||
/// @arg `LensMode`
|
||||
/// @arg `ScientaChannelBegin`
|
||||
/// @arg `ScientaChannelEnd`
|
||||
/// @arg `ScientaSliceBegin`
|
||||
/// @arg `ScientaSliceEnd`
|
||||
/// @arg `ScanWritables`
|
||||
/// @arg wave referenced by `ScanWritables[0]`
|
||||
///
|
||||
@ -1456,6 +1607,9 @@ end
|
||||
///
|
||||
/// @return the function results are written to the lo, hi, un, and ax waves.
|
||||
///
|
||||
/// @version this function supports regions from version 1.03.
|
||||
/// check that you're in the correct data folder!
|
||||
///
|
||||
function ps_detect_scale(ax, lo, hi, un)
|
||||
wave /t ax
|
||||
wave lo
|
||||
@ -1463,7 +1617,8 @@ function ps_detect_scale(ax, lo, hi, un)
|
||||
wave /t un
|
||||
|
||||
dfref dataDF = GetDataFolderDFR()
|
||||
dfref attrDF = :attr
|
||||
dfref scanDF = find_scan_folder(dataDF)
|
||||
dfref attrDF = find_attr_folder(dataDF)
|
||||
|
||||
redimension /n=4 lo, hi, un, ax
|
||||
setdimlabel 0, 0, $kEnergyDimLabel, lo, hi, un, ax
|
||||
@ -1493,10 +1648,10 @@ function ps_detect_scale(ax, lo, hi, un)
|
||||
ax[%$kDataDimLabel] = "value"
|
||||
|
||||
wave /SDFR=attrDF /T /Z LensMode
|
||||
wave /SDFR=attrDF /Z ChannelBegin = ScientaChannelBegin
|
||||
wave /SDFR=attrDF /Z ChannelEnd = ScientaChannelEnd
|
||||
wave /SDFR=attrDF /Z SliceBegin = ScientaSliceBegin
|
||||
wave /SDFR=attrDF /Z SliceEnd = ScientaSliceEnd
|
||||
wave /Z ChannelBegin = find_scale_wave("ScientaChannelBegin", dataDF, scanDF, attrDF)
|
||||
wave /Z ChannelEnd = find_scale_wave("ScientaChannelEnd", dataDF, scanDF, attrDF)
|
||||
wave /Z SliceBegin = find_scale_wave("ScientaSliceBegin", dataDF, scanDF, attrDF)
|
||||
wave /Z SliceEnd = find_scale_wave("ScientaSliceEnd", dataDF, scanDF, attrDF)
|
||||
|
||||
// lens mode can give more detail
|
||||
if (waveexists(LensMode) && (numpnts(LensMode) >= 1))
|
||||
@ -1504,13 +1659,13 @@ function ps_detect_scale(ax, lo, hi, un)
|
||||
case "Angular45":
|
||||
lo[%$kAngleDimLabel] = -45/2
|
||||
hi[%$kAngleDimLabel] = +45/2
|
||||
un[%$kAngleDimLabel] = "deg"
|
||||
un[%$kAngleDimLabel] = "°"
|
||||
ax[%$kAngleDimLabel] = "angle"
|
||||
break
|
||||
case "Angular60":
|
||||
lo[%$kAngleDimLabel] = -60/2
|
||||
hi[%$kAngleDimLabel] = +60/2
|
||||
un[%$kAngleDimLabel] = "deg"
|
||||
un[%$kAngleDimLabel] = "°"
|
||||
ax[%$kAngleDimLabel] = "angle"
|
||||
break
|
||||
case "Transmission":
|
||||
@ -1529,9 +1684,10 @@ function ps_detect_scale(ax, lo, hi, un)
|
||||
lo[%$kAngleDimLabel] = SliceBegin[0]
|
||||
hi[%$kAngleDimLabel] = SliceEnd[0]
|
||||
endif
|
||||
wave /z /t /SDFR=dataDF ScanWritables
|
||||
|
||||
wave /z /t /SDFR=scanDF ScanWritables
|
||||
if (WaveExists(ScanWritables))
|
||||
wave /z /SDFR=dataDF scanner = $ScanWritables[0]
|
||||
wave /z /SDFR=scanDF scanner = $ScanWritables[0]
|
||||
if (!WaveExists(scanner))
|
||||
wave /z /SDFR=attrDF scanner = $ScanWritables[0]
|
||||
endif
|
||||
@ -1553,6 +1709,7 @@ function ps_detect_scale(ax, lo, hi, un)
|
||||
case "RefocusZTrans":
|
||||
case "ExitSlitY":
|
||||
un[%$kScanDimLabel] = "mm"
|
||||
break
|
||||
case "ExitSlit":
|
||||
un[%$kScanDimLabel] = "µm"
|
||||
break
|
||||
@ -1560,6 +1717,7 @@ function ps_detect_scale(ax, lo, hi, un)
|
||||
case "ManipulatorTilt":
|
||||
case "ManipulatorPhi":
|
||||
un[%$kScanDimLabel] = "°"
|
||||
break
|
||||
case "FocusXRot":
|
||||
case "FocusYRot":
|
||||
case "FocusZRot":
|
||||
@ -1567,6 +1725,7 @@ function ps_detect_scale(ax, lo, hi, un)
|
||||
case "RefocusYRot":
|
||||
case "RefocusZRot":
|
||||
un[%$kScanDimLabel] = "mrad"
|
||||
break
|
||||
endswitch
|
||||
endif
|
||||
endif
|
||||
@ -1603,6 +1762,8 @@ end
|
||||
/// @param un unit labels.
|
||||
/// the unit labels are applied using the SetScale operation.
|
||||
///
|
||||
/// @version this function supports regions from version 1.03.
|
||||
///
|
||||
function ps_scale_dataset_2(data, ax, lo, hi, un)
|
||||
wave data
|
||||
wave /t ax
|
||||
@ -1746,8 +1907,11 @@ function /s psh5_load_reduced(ANickName, APathName, AFileName, reduction_func, r
|
||||
HDF5LoadData /O /Q /Z fileID, positionerpath
|
||||
endif
|
||||
endif
|
||||
|
||||
setdatafolder dataDF
|
||||
wavenames = psh5_load_dataset_reduced(fileID, scanpath, "ScientaImage", reduction_func, reduction_param, progress=progress)
|
||||
string datasets = psh5_list_scan_datasets(fileID, scanpath, include_regions=1)
|
||||
string dataset = select_dataset(datasets, "ScientaImage")
|
||||
wavenames = psh5_load_dataset_reduced(fileID, scanpath, dataset, reduction_func, reduction_param, progress=progress)
|
||||
|
||||
psh5_close_file(fileID)
|
||||
endif
|
||||
@ -1783,7 +1947,10 @@ end
|
||||
///
|
||||
/// @param scanpath path to scan group in the HDF5 file.
|
||||
///
|
||||
/// @param dataset name of the dataset.
|
||||
/// @param datasetname name of the dataset.
|
||||
/// the name of the loaded wave is a cleaned up version of the dataset name.
|
||||
/// the name can include the region name as a relative path, e.g. "region1/ScientaSpectrum".
|
||||
/// in this case, the dataset is loaded into a sub-folder named "region1".
|
||||
///
|
||||
/// @param reduction_func custom reduction function
|
||||
/// (any user-defined function which has the same parameters as adh5_default_reduction()).
|
||||
@ -1804,6 +1971,8 @@ end
|
||||
/// empty string if an error occurred.
|
||||
/// error messages are printed to the history.
|
||||
///
|
||||
/// @version this function supports regions as of version 1.03.
|
||||
///
|
||||
function /s psh5_load_dataset_reduced(fileID, scanpath, datasetname, reduction_func, reduction_param, [progress, nthreads])
|
||||
variable fileID
|
||||
string scanpath
|
||||
@ -1820,6 +1989,7 @@ function /s psh5_load_dataset_reduced(fileID, scanpath, datasetname, reduction_f
|
||||
nthreads = -1
|
||||
endif
|
||||
|
||||
dfref base_df = GetDataFolderDFR()
|
||||
variable result = 0
|
||||
string datasetpath
|
||||
string datawavename
|
||||
@ -1829,6 +1999,18 @@ function /s psh5_load_dataset_reduced(fileID, scanpath, datasetname, reduction_f
|
||||
datasetpath = ReplaceString("//", datasetpath, "/")
|
||||
datawavename = StringFromList(ItemsInList(datasetpath, "/") - 1, datasetpath, "/")
|
||||
|
||||
string regionname
|
||||
string regionpath
|
||||
if (ItemsInList(datasetname, "/") >= 2)
|
||||
regionname = StringFromList(0, datasetname, "/")
|
||||
regionpath = ReplaceString("//", scanpath + "/" + regionname, "/")
|
||||
datasetname = RemoveListItem(0, datasetname, "/")
|
||||
NewDataFolder /o/s $regionname
|
||||
else
|
||||
regionname = ""
|
||||
regionpath = scanpath
|
||||
endif
|
||||
|
||||
STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf.
|
||||
InitHDF5DataInfo(di)
|
||||
variable err = HDF5DatasetInfo(fileID, datasetpath, 0, di)
|
||||
@ -2035,6 +2217,7 @@ function /s psh5_load_dataset_reduced(fileID, scanpath, datasetname, reduction_f
|
||||
kill_progress_panel()
|
||||
endif
|
||||
|
||||
setdatafolder base_df
|
||||
return wavenames
|
||||
end
|
||||
|
||||
|
||||
Binary file not shown.
Loading…
x
Reference in New Issue
Block a user