CalcImage CIP project file format

[John Donovan]

I thought it might be useful to post the read/write code for the CalcImage CIP project file format.  This is the text file that CalcImage uses to store all information (not contained in the PFE MDB file), for defining a quantitative mapping project.

For example to help Ben Buse here:

Also need to figure out how to load files into calcimage best.

At moment I'm creating a new blank project in calcimage and then loading each of the files as grd files. Is there a better way of doing this.

I tried loading the wds elements through the create project wizzard. But when I added eds grd files at the end, it said must be added before off peak maps.

So here is the code for reading and then, writing a CalcImage CIP project file:

Code Select Expand

Sub CalcImageReadWriteProjectFile(mode As Integer)
' Read or write the project file
'  mode = 1 read project
'  mode = 2 write project

ierror = False
On Error GoTo CalcImageReadWriteProjectFileError

Dim i As Integer, tFlag As Integer, j As Integer
Dim itemp6 As Integer
Dim tfilename As String
Dim astring As String, bstring As String

' Read project
If mode% = 1 Then

' Init project
Call CalcImageInitProject(Int(0))
If ierror Then Exit Sub

' Check for version of CIP file for reading only!
CalcImageProjectVersion% = CalcImageGetProjectFileVersion()
If ierror Then Exit Sub

' If file version is zero, call special routine for backward compatibility (write project uses current version)
If CalcImageProjectVersion% = 0 Then
Call CalcImageReadVersionZeroCIPFile(mode%)
If ierror Then Exit Sub
Exit Sub
End If

' Project file contains full path, but condition and image files do not (must be in same folder as CIP and MDB file)
Open CalcImageProjectFile$ For Input As #CalcImageProjectFileNumber%

Input #CalcImageProjectFileNumber%, CalcImageProjectVersion%, CalcImageProjectTitle$

' Check that CIP file is not a newer version
If CalcImageProjectVersion% > CIP_FILE_VERSION% Then GoTo CalcImageReadWriteProjectFileNewerCIPFile

' If version 2, read CalcImageSampleNameTitle field
If CalcImageProjectVersion% >= 2 Then
Input #CalcImageProjectFileNumber%, CalcImageSampleNameTitle$
End If

' Read and load probe data file name
Input #CalcImageProjectFileNumber%, tfilename$
tfilename$ = MiscGetPathOnly$(CalcImageProjectFile$) & tfilename$

' Check for files existing
If Trim$(tfilename$) = vbNullString Then GoTo CalcImageReadWriteProjectFileBlankCondition
If Dir$(tfilename$) = vbNullString Then GoTo CalcImageReadWriteProjectFileMissingCondition

' Load Probe database file name (full path)
ProbeDataFile$ = tfilename$
Line Input #CalcImageProjectFileNumber%, astring$   ' read entire parameter line and parse each parameter (for backward compatibility)

' Read sample number
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageProbeDataSample% = Val(bstring$)

' Read number of images
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageNumberofImageFiles% = Val(bstring$)
If CalcImageNumberofImageFiles% > MAXIMAGE% Then GoTo CalcImageReadWriteProjectFileTooManyImages

' Read CalcImageCalculateTotalsImageFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateTotalsImageFlag% = Val(bstring$)

' Read CalcImageCalculateStoichiometricOxygenImageFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateStoichiometricOxygenImageFlag% = Val(bstring$)

Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateExcessOxygenImageFlag% = Val(bstring$)

' Read CalcImageCalculateNetIntensitiesFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateNetIntensitiesFlag% = Val(bstring$)

' Read CalcImageCalculateBgdIntensitiesFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateBgdIntensitiesFlag% = Val(bstring$)

' Read CalcImageCalculateKratioIntensitiesFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateKratioIntensitiesFlag% = Val(bstring$)

' Read CalcImageCalculateQuantPercentsFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateQuantPercentsFlag% = Val(bstring$)

' Read CalcImageCalculateAtomicPercentsFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateAtomicPercentsFlag% = Val(bstring$)

' Read CalcImageCalculateOxidePercentsFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateOxidePercentsFlag% = Val(bstring$)

' Read CalcImageCalculateFormulaBasisFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateFormulaBasisFlag% = Val(bstring$)

' Read CalcImageCalculateElementByDiffImageFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateElementByDiffImageFlag% = Val(bstring$)

' Read CalcImageCalculateDetectionLimitsFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateDetectionLimitsFlag% = Val(bstring$)

' Read CalcImageCalculateAnalyticalSensitivityFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateAnalyticalSensitivityFlag% = Val(bstring$)

' Read CalcImageCalculateLogWeightPercentsFlag
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateLogWeightPercentsFlag% = Val(bstring$)

' Read CalcImageCalculateDetectionLimitsBlankingFlag (new)
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateDetectionLimitsBlankingFlag% = Val(bstring$)

' Read CalcImageCalculateAnalyticalSensitivityBlankingFlag (new)
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageCalculateAnalyticalSensitivityBlankingFlag% = Val(bstring$)

' Read CalcImageBlankValuesOutsideMinMaxAnalyticalTotalFlag (new)
Call MiscParseStringToStringA(astring$, VbSpace, bstring$)
If ierror Then Exit Sub
CalcImageBlankValuesOutsideMinMaxAnalyticalTotalFlag% = Val(bstring$)

' To ensure that the elemental quant flag is always set
CalcImageCalculateQuantPercentsFlag% = -1   ' always calculate elemental percents!

' Read image files (count time is no longer utilized since intensity data is in cps from PI)
For i% = 1 To CalcImageNumberofImageFiles%
If CalcImageProjectVersion% <= 9 Then
Input #CalcImageProjectFileNumber%, CalcImageImageTypes%(i%), CalcImageElementRows%(i%), CalcImageCountTimes!(i%), CalcImageBeamCurrents!(i%), CalcImageBeamCurrents2!(i%), CalcImageTimeOfAcqs#(i%), CalcImageTimeOfAcqs2#(i%), CalcImageImageFiles$(i%)
Else
Input #CalcImageProjectFileNumber%, CalcImageImageTypes%(i%), CalcImageElementRows%(i%), CalcImageCountTimes!(i%), CalcImageBeamCurrents!(i%), CalcImageBeamCurrents2!(i%), CalcImageTimeOfAcqs#(i%), CalcImageTimeOfAcqs2#(i%), CalcImageImageFiles$(i%), CalcImageImagePositions!(i%)
End If
CalcImageImageFiles$(i%) = MiscGetPathOnly$(CalcImageProjectFile$) & CalcImageImageFiles$(i%)
Next i%

' Now read CPQ files and parameters
Call CalcImageCPQReadWriteProjectFile(mode%, CalcImageProjectFileNumber%)
If ierror Then Exit Sub

' If version 3, read misc parameters array (6 integers)
If CalcImageProjectVersion% >= 3 Then
Input #CalcImageProjectFileNumber%, CalcImageTitleAppendDataFlag%, CalcImageSurferOutputTemplateFlag%, CalcImageSurferSliceTemplateFlag%, CalcImageSurferPolygonTemplateFlag%, CalcImageSurferStripTemplateFlag%, UseManualAssignmentModeFlag%, itemp6%
End If

' If version 4, read EDS spectrum image flag (not utilized yet) and filename
If CalcImageProjectVersion% >= 4 Then
Input #CalcImageProjectFileNumber%, tFlag%, IntegrateEDSSpectrumImagingFilename$
End If

' If version 5, read scan type (0 = beam scan, 1 = stage scan) and scan orientation type (0 = Cameca stage/beam or JEOL beam scan (UL/LR), 1 = JEOL stage scan (UR/LL))
If CalcImageProjectVersion% >= 5 Then
Input #CalcImageProjectFileNumber%, CalcImageScanTypeFlag%, CalcImageOrientationTypeFlag%
End If

' If version 6, read analog signal image output flags and names
If CalcImageProjectVersion% >= 6 Then
Input #CalcImageProjectFileNumber%, CalcImageAnalogSignalFlags(1), CalcImageAnalogSignalLabels(1), CalcImageAnalogSignalFlags(2), CalcImageAnalogSignalLabels(2), CalcImageAnalogSignalFlags(3), CalcImageAnalogSignalLabels(3)
End If

' If version 7, read analog signal image filenames
If CalcImageProjectVersion% >= 7 Then
Input #CalcImageProjectFileNumber%, AnalogFilenames$(1), AnalogFilenames$(2), AnalogFilenames$(3)
If Trim$(AnalogFilenames$(1)) <> vbNullString Then AnalogFilenames$(1) = MiscGetPathOnly$(CalcImageProjectFile$) & AnalogFilenames$(1)
If Trim$(AnalogFilenames$(2)) <> vbNullString Then AnalogFilenames$(2) = MiscGetPathOnly$(CalcImageProjectFile$) & AnalogFilenames$(2)
If Trim$(AnalogFilenames$(3)) <> vbNullString Then AnalogFilenames$(3) = MiscGetPathOnly$(CalcImageProjectFile$) & AnalogFilenames$(3)
End If

' If version 8, read number of TDI files and number of intervals
If CalcImageProjectVersion% >= 8 Then
Input #CalcImageProjectFileNumber%, CalcImageNumberOfTDIImageFiles%, CalcImageNumberOfTDIImageIntervals%
For i% = 1 To CalcImageNumberOfTDIImageFiles%
Input #CalcImageProjectFileNumber%, CalcImageTDIImageIntervals%(i%), CalcImageTDIElementRows%(i%), CalcImageTDICountTimes!(i%), CalcImageTDIBeamCurrents!(i%), CalcImageTDIBeamCurrents2!(i%), CalcImageTDITimeOfAcqs#(i%), CalcImageTDITimeOfAcqs2#(i%), CalcImageTDIImageFiles$(i%)
CalcImageTDIImageFiles$(i%) = MiscGetPathOnly$(CalcImageProjectFile$) & CalcImageTDIImageFiles$(i%)
Next i%
End If

' If version 9, read output matrix corrections flag and unused flags
If CalcImageProjectVersion% >= 9 Then
Input #CalcImageProjectFileNumber%, CalcImageCalculateMatrixCorrectionsFlag%, tFlag%, tFlag%, tFlag%, tFlag%, tFlag%
End If

' If version 11, read dynamic element parameters (version 10 is above for image files- spectrometer positions)
If CalcImageProjectVersion% >= 11 Then
Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementByDifferenceFlag%
For j% = 1 To MAXCRITERIA%
Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementByDifferenceElement%(j%), DynamicSpecifiedElementByDifferenceValue!(j%), DynamicSpecifiedElementByDifferenceGreaterLess%(j%)
Next j%
Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementByDifferenceOperator1%, DynamicSpecifiedElementByDifferenceOperator2%

Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementByDifferenceFormulaFlag%
For j% = 1 To MAXCRITERIA%
Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementByDifferenceFormulaElement%(j%), DynamicSpecifiedElementByDifferenceFormulaValue!(j%), DynamicSpecifiedElementByDifferenceFormulaGreaterLess%(j%)
Next j%
Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementByDifferenceFormulaOperator1%, DynamicSpecifiedElementByDifferenceFormulaOperator2%

Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementByStoichiometryToOxygenFlag%
For j% = 1 To MAXCRITERIA%
Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementByStoichiometryToOxygenElement%(j%), DynamicSpecifiedElementByStoichiometryToOxygenValue!(j%), DynamicSpecifiedElementByStoichiometryToOxygenGreaterLess%(j%)
Next j%
Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementByStoichiometryToOxygenOperator1%, DynamicSpecifiedElementByStoichiometryToOxygenOperator2%

Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementByStoichiometryToAnotherFlag%
For j% = 1 To MAXCRITERIA%
Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementByStoichiometryToAnotherElement%(j%), DynamicSpecifiedElementByStoichiometryToAnotherValue!(j%), DynamicSpecifiedElementByStoichiometryToAnotherGreaterLess%(j%)
Next j%
Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementByStoichiometryToAnotherOperator1%, DynamicSpecifiedElementByStoichiometryToAnotherOperator2%

Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementExcessOxygenByDroopFlag%
For j% = 1 To MAXCRITERIA%
Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementExcessOxygenByDroopElement%(j%), DynamicSpecifiedElementExcessOxygenByDroopValue!(j%), DynamicSpecifiedElementExcessOxygenByDroopGreaterLess%(j%)
Next j%
Input #CalcImageProjectFileNumber%, DynamicSpecifiedElementExcessOxygenByDroopOperator1%, DynamicSpecifiedElementExcessOxygenByDroopOperator2%
End If

' If version 12, read dynamic oxygen by stoichiometry parameters
If CalcImageProjectVersion% >= 12 Then
Input #CalcImageProjectFileNumber%, DynamicOxygenByStoichiometryFlag%
For j% = 1 To MAXCRITERIA%
Input #CalcImageProjectFileNumber%, DynamicOxygenByStoichiometryElement%(j%), DynamicOxygenByStoichiometryValue!(j%), DynamicOxygenByStoichiometryGreaterLess%(j%)
Next j%
Input #CalcImageProjectFileNumber%, DynamicOxygenByStoichiometryOperator1%, DynamicOxygenByStoichiometryOperator2%
End If

Close #CalcImageProjectFileNumber%

' Check for blank title
If Trim$(CalcImageProjectTitle$) = vbNullString Then CalcImageProjectTitle$ = "CalcImage Quantitative Image Project " & Now

' Check for blank file names
For i% = 1 To CalcImageNumberofImageFiles%
If Trim$(CalcImageImageFiles$(i%)) = vbNullString Then GoTo CalcImageReadWriteProjectFileBlankImage
If Dir$(CalcImageImageFiles$(i%)) = vbNullString Then GoTo CalcImageReadWriteProjectFileMissingImage
Next i%

End If


' Write project
If mode% = 2 Then

' Update CIP project file to current version
CalcImageProjectVersion% = CIP_FILE_VERSION%

' Check for files existing
If Trim$(ProbeDataFile$) = vbNullString Then GoTo CalcImageReadWriteProjectFileBlankCondition
If Dir$(ProbeDataFile$) = vbNullString Then GoTo CalcImageReadWriteProjectFileMissingCondition

For i% = 1 To CalcImageNumberofImageFiles%
If Trim$(CalcImageImageFiles$(i%)) = vbNullString Then GoTo CalcImageReadWriteProjectFileBlankImage
If Dir$(CalcImageImageFiles$(i%)) = vbNullString Then GoTo CalcImageReadWriteProjectFileMissingImage
Next i%

' Check for blank title
If Trim$(CalcImageProjectTitle$) = vbNullString Then CalcImageProjectTitle$ = "CalcImage Quantitative Image Project " & Now

If CalcImageNumberofImageFiles% > MAXIMAGE% Then GoTo CalcImageReadWriteProjectFileTooManyImages

' Project file does not contain full path (uses current CIP folder)
Open CalcImageProjectFile$ For Output As #CalcImageProjectFileNumber%

Print #CalcImageProjectFileNumber%, CalcImageProjectVersion%, VbDquote$ & CalcImageProjectTitle$ & VbDquote$
Print #CalcImageProjectFileNumber%, VbDquote$ & CalcImageSampleNameTitle$ & VbDquote$
Print #CalcImageProjectFileNumber%, VbDquote$ & MiscGetFileNameOnly$(ProbeDataFile$) & VbDquote$
Print #CalcImageProjectFileNumber%, CalcImageProbeDataSample%, CalcImageNumberofImageFiles%, CalcImageCalculateTotalsImageFlag%, CalcImageCalculateStoichiometricOxygenImageFlag%, CalcImageCalculateExcessOxygenImageFlag%, CalcImageCalculateNetIntensitiesFlag%, CalcImageCalculateBgdIntensitiesFlag%, CalcImageCalculateKratioIntensitiesFlag%, CalcImageCalculateQuantPercentsFlag%, CalcImageCalculateAtomicPercentsFlag%, CalcImageCalculateOxidePercentsFlag%, CalcImageCalculateFormulaBasisFlag%, CalcImageCalculateElementByDiffImageFlag%, CalcImageCalculateDetectionLimitsFlag%, CalcImageCalculateAnalyticalSensitivityFlag%, CalcImageCalculateLogWeightPercentsFlag%, CalcImageCalculateDetectionLimitsBlankingFlag%, CalcImageCalculateAnalyticalSensitivityBlankingFlag%, CalcImageBlankValuesOutsideMinMaxAnalyticalTotalFlag%

' Write on and off peak image files
For i% = 1 To CalcImageNumberofImageFiles%
If CalcImageProjectVersion% <= 9 Then
Print #CalcImageProjectFileNumber%, CalcImageImageTypes%(i%), CalcImageElementRows%(i%), Format$(CalcImageCountTimes!(i%), f83$), CalcImageBeamCurrents!(i%), CalcImageBeamCurrents2!(i%), CalcImageTimeOfAcqs#(i%), CalcImageTimeOfAcqs2#(i%), VbDquote$ & MiscGetFileNameOnly$(CalcImageImageFiles$(i%)) & VbDquote$
Else
Print #CalcImageProjectFileNumber%, CalcImageImageTypes%(i%), CalcImageElementRows%(i%), Format$(CalcImageCountTimes!(i%), f83$), CalcImageBeamCurrents!(i%), CalcImageBeamCurrents2!(i%), CalcImageTimeOfAcqs#(i%), CalcImageTimeOfAcqs2#(i%), VbDquote$ & MiscGetFileNameOnly$(CalcImageImageFiles$(i%)) & VbDquote$, CalcImageImagePositions!(i%)
End If
Next i%

' Now write CPQ files and parameters
Call CalcImageCPQReadWriteProjectFile(mode%, CalcImageProjectFileNumber%)
If ierror Then Exit Sub

' Now write misc parameters
Print #CalcImageProjectFileNumber%, CalcImageTitleAppendDataFlag%, CalcImageSurferOutputTemplateFlag%, CalcImageSurferSliceTemplateFlag%, CalcImageSurferPolygonTemplateFlag%, CalcImageSurferStripTemplateFlag%, UseManualAssignmentModeFlag, itemp6%

' Now write EDS spectrum image flag (not utilized yet) and filename
Print #CalcImageProjectFileNumber%, tFlag%, VbDquote$ & IntegrateEDSSpectrumImagingFilename$ & VbDquote$

' Now write scan type (0 = beam scan, 1 = stage scan) and scan orientation type (0 = Cameca stage/beam or JEOL beam scan (UL/LR), 1 = JEOL stage scan (UR/LL))
Print #CalcImageProjectFileNumber%, CalcImageScanTypeFlag%, CalcImageOrientationTypeFlag%

' Now write analog signal image output flags and names
Print #CalcImageProjectFileNumber%, CalcImageAnalogSignalFlags(1), VbDquote$ & CalcImageAnalogSignalLabels(1) & VbDquote, CalcImageAnalogSignalFlags(2), VbDquote$ & CalcImageAnalogSignalLabels(2) & VbDquote, CalcImageAnalogSignalFlags(3), VbDquote$ & CalcImageAnalogSignalLabels(3) & VbDquote

' Now write analog signal file names
Print #CalcImageProjectFileNumber%, VbDquote$ & MiscGetFileNameOnly$(AnalogFilenames$(1)) & VbDquote$, VbDquote$ & MiscGetFileNameOnly$(AnalogFilenames$(2)) & VbDquote$, VbDquote$ & MiscGetFileNameOnly$(AnalogFilenames$(3)) & VbDquote$

' Now write number of TDI files and number of TDI intervals
Print #CalcImageProjectFileNumber%, CalcImageNumberOfTDIImageFiles%, CalcImageNumberOfTDIImageIntervals%

' Write TDI image files
For i% = 1 To CalcImageNumberOfTDIImageFiles%
Print #CalcImageProjectFileNumber%, CalcImageTDIImageIntervals%(i%), CalcImageTDIElementRows%(i%), Format$(CalcImageTDICountTimes!(i%), f83$), CalcImageTDIBeamCurrents!(i%), CalcImageTDIBeamCurrents2!(i%), CalcImageTDITimeOfAcqs#(i%), CalcImageTDITimeOfAcqs2#(i%), VbDquote & MiscGetFileNameOnly$(CalcImageTDIImageFiles$(i%)) & VbDquote
Next i%

' Write newest calculation flags
Print #CalcImageProjectFileNumber%, CalcImageCalculateMatrixCorrectionsFlag%, tFlag%, tFlag%, tFlag%, tFlag%, tFlag%

' Write dynamic element parameters
Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementByDifferenceFlag%
For j% = 1 To MAXCRITERIA%
Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementByDifferenceElement%(j%), DynamicSpecifiedElementByDifferenceValue!(j%), DynamicSpecifiedElementByDifferenceGreaterLess%(j%)
Next j%
Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementByDifferenceOperator1%, DynamicSpecifiedElementByDifferenceOperator2%

Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementByDifferenceFormulaFlag%
For j% = 1 To MAXCRITERIA%
Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementByDifferenceFormulaElement%(j%), DynamicSpecifiedElementByDifferenceFormulaValue!(j%), DynamicSpecifiedElementByDifferenceFormulaGreaterLess%(j%)
Next j%
Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementByDifferenceFormulaOperator1%, DynamicSpecifiedElementByDifferenceFormulaOperator2%

Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementByStoichiometryToOxygenFlag%
For j% = 1 To MAXCRITERIA%
Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementByStoichiometryToOxygenElement%(j%), DynamicSpecifiedElementByStoichiometryToOxygenValue!(j%), DynamicSpecifiedElementByStoichiometryToOxygenGreaterLess%(j%)
Next j%
Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementByStoichiometryToOxygenOperator1%, DynamicSpecifiedElementByStoichiometryToOxygenOperator2%

Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementByStoichiometryToAnotherFlag%
For j% = 1 To MAXCRITERIA%
Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementByStoichiometryToAnotherElement%(j%), DynamicSpecifiedElementByStoichiometryToAnotherValue!(j%), DynamicSpecifiedElementByStoichiometryToAnotherGreaterLess%(j%)
Next j%
Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementByStoichiometryToAnotherOperator1%, DynamicSpecifiedElementByStoichiometryToAnotherOperator2%

Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementExcessOxygenByDroopFlag%
For j% = 1 To MAXCRITERIA%
Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementExcessOxygenByDroopElement%(j%), DynamicSpecifiedElementExcessOxygenByDroopValue!(j%), DynamicSpecifiedElementExcessOxygenByDroopGreaterLess%(j%)
Next j%
Print #CalcImageProjectFileNumber%, DynamicSpecifiedElementExcessOxygenByDroopOperator1%, DynamicSpecifiedElementExcessOxygenByDroopOperator2%

' Write dynamic oxygen by stoichiometry parameters
Print #CalcImageProjectFileNumber%, DynamicOxygenByStoichiometryFlag%
For j% = 1 To MAXCRITERIA%
Print #CalcImageProjectFileNumber%, DynamicOxygenByStoichiometryElement%(j%), DynamicOxygenByStoichiometryValue!(j%), DynamicOxygenByStoichiometryGreaterLess%(j%)
Next j%
Print #CalcImageProjectFileNumber%, DynamicOxygenByStoichiometryOperator1%, DynamicOxygenByStoichiometryOperator2%

Close #CalcImageProjectFileNumber%
End If

Exit Sub

' Errors
CalcImageReadWriteProjectFileError:
CalcImageProjectFile$ = vbNullString
CalcImageSampleNameTitle$ = vbNullString
MsgBox Error$, vbOKOnly + vbCritical, "CalcImageReadWriteProjectFile"
Close #CalcImageProjectFileNumber%
ierror = True
Exit Sub

CalcImageReadWriteProjectFileNewerCIPFile:
msg$ = "CalcImage CIP file (" & CalcImageProjectFile$ & ") version (" & Format$(CalcImageProjectVersion%) & ") was created by a newer version of the CalcImage application. Please update Probe for EPMA to get the most recent version of CalcImage"
MsgBox msg$, vbOKOnly + vbExclamation, "CalcImageReadWriteProjectFile"
Close #CalcImageProjectFileNumber%
ProbeDataFile$ = vbNullString
ierror = True
Exit Sub

CalcImageReadWriteProjectFileBlankCondition:
msg$ = "Probe data file name is blank in CalcImage Project File " & CalcImageProjectFile$
MsgBox msg$, vbOKOnly + vbExclamation, "CalcImageReadWriteProjectFile"
Close #CalcImageProjectFileNumber%
ProbeDataFile$ = vbNullString
ierror = True
Exit Sub

CalcImageReadWriteProjectFileMissingCondition:
msg$ = "Probe data file " & tfilename$ & " is missing"
MsgBox msg$, vbOKOnly + vbExclamation, "CalcImageReadWriteProjectFile"
Close #CalcImageProjectFileNumber%
CalcImageProjectFile$ = vbNullString
CalcImageSampleNameTitle$ = vbNullString
ierror = True
Exit Sub

CalcImageReadWriteProjectFileTooManyImages:
msg$ = "Too many image files specified in CalcImage Project File " & CalcImageProjectFile$
MsgBox msg$, vbOKOnly + vbExclamation, "CalcImageReadWriteProjectFile"
Close #CalcImageProjectFileNumber%
CalcImageProjectFile$ = vbNullString
CalcImageSampleNameTitle$ = vbNullString
ierror = True
Exit Sub

CalcImageReadWriteProjectFileBlankImage:
msg$ = "Image file number " & Str$(i%) & " name is blank in CalcImage Project File " & CalcImageProjectFile$
MsgBox msg$, vbOKOnly + vbExclamation, "CalcImageReadWriteProjectFile"
Close #CalcImageProjectFileNumber%
CalcImageProjectFile$ = vbNullString
CalcImageSampleNameTitle$ = vbNullString
ierror = True
Exit Sub

CalcImageReadWriteProjectFileMissingImage:
msg$ = "Image file " & CalcImageImageFiles$(i%) & " is missing"
MsgBox msg$, vbOKOnly + vbExclamation, "CalcImageReadWriteProjectFile"
Close #CalcImageProjectFileNumber%
CalcImageProjectFile$ = vbNullString
CalcImageSampleNameTitle$ = vbNullString
ierror = True
Exit Sub

End Sub

Note that additional explanation is provided in the CalcImage Help file:



which can be accessed from the CalcImage Help menu.

[Ben Buse]

Thanks for this post and the help file flag.

I'm just working through programming it in python.

I love this entry in the file definition, it made me smile

Code Select Expand

The next line contains flags for output of analog signal images:

0            "SE"          0            "BSE"          0            "CL"

"MSH4-1_00653_VS1.grd"      ""            ""

 

It's pretty self explanatory



What do the zeros mean in first line?
Second line is a list of the file names, does "" mean no file present

here's the code so far

Code Select Expand

#where only one set of maps in folder
#where uses last sample in mdb
#where mdb in same folder and only one mdb present
import tkinter
from tkinter import filedialog
from numpy import genfromtxt
import datetime
import pyodbc
cndfile = tkinter.filedialog.askopenfile(title="Select WDS element .cnd file")
reader = csv.reader(open(cndfile.name), delimiter=" ")
d = list(reader)
path = filedialog.askdirectory(title="Select location of csv kratio map files")
fc = open(path + '/' + 'test cip creation.cip','w')
fc.write('12'+'           '+'"'+'CalcImage Quantitative Image Project'+' '+datetime.datetime.now().strftime("%x")+' '+datetime.datetime.now().strftime("%X")+'"')
for fileMDB in glob.glob(os.path.join(path,'*.MDB')):
    print(fileMDB)
MDBname = re.sub("[]'[]",'',fileMDB.split('\\')[1]).split('.MDB')[0]
fc.write('"'+MDBname+'_'+ProjectName+'00001_'+'"')
fc.write('"'+MDBfile+'"')
MDB = fileMDB
DRV = 'Microsoft Access Driver (*.mdb, *.accdb)'
PWD = 'pw'
con = pyodbc.connect('DRIVER={};DBQ={};PWD={}'.format(DRV,MDB,PWD))
cur = con.cursor()
SQL = 'SELECT * FROM Sample;'
rows = cur.execute(SQL).fetchall()
LastSample = len(rows)
cur.close()
con.close()
MapCounter = len(glob.glob1(path,'*_.grd'))
MapCounterEDS = len(glob.glob1(path,'*EDS.grd'))
#MinusOxygen = 1
MapCounterPOFF = len(glob.glob1(path,'*POFF.grd'))
MapCounterNOFF = len(glob.glob1(path,'*NOFF.grd'))
#NumMaps = MapCounter+MapCounterEDS-MinusOxygen
NumMaps = MapCounter+MapCounterEDS+MapCounterPOFF+MapCounterNOFF
TotalsImageFlag = -1
StoicOxFlag = -1
ExcessOxFlag = 0
NetIntenFlag = 0
BgdIntenFlag = 0
KratioIntenFlag = 0
QuantPercFlag = -1
AtomPercFlag = 0
OxidePercFlag = -1
FormulaBasisFlag = 0
EleDiffFlag = 0
DetLimFlag = 0
ErrorFlag = 0
LogPctFlag = 0
DLBlankFlag = 0
ErrBlankFlag = 0
Final = 0
sub = '$XM_AP_SA_DWELL_TIME%0'
WDSDwell = [s for s in d if sub in s][0][1]
sub2 = '$XM_DATA_SAVE_DATE'
offset = 693594
#exceldate = datetime.datetime.date(datetime.datetime.strptime([s for s in d if sub2 in s][0][1],"%Y/%m/%d")).toordinal()-offset
exceltim = datetime.datetime(1899,12,30)
cnddatetime=[s for s in d if sub2 in s][0][1]+' '+[s for s in d if sub2 in s][0][2]
delta=datetime.datetime.strptime(cnddatetime,'%Y/%m/%d %H:%M:%S')-exceltim
excelstore = float(delta.days)+(float(delta.seconds)/86400)
sub3 = '$XM_CP_DATE'
cnddatetime3=[s for s in d if sub3 in s][0][1]+' '+[s for s in d if sub3 in s][0][2]
delta3=datetime.datetime.strptime(cnddatetime3,'%Y/%m/%d %H:%M:%S')-exceltim
excelstore3 = float(delta3.days)+(float(delta3.seconds)/86400)
fc.write(str(LastSample)+spacer+str(NumMaps)+spacer+str(TotalsImageFlag)+spacer+str(StoicOxFlag)+spacer+str(ExcessOxFlag)+spacer+str(NetIntenFlag)+spacer+str(BgdIntenFlag)+spacer+str(KratioIntenFlag)+spacer+str(QuantPercFlag)+spacer+str(AtomPercFlag)+spacer+str(OxidePercFlag)+spacer+str(FormulaBasisFlag)+spacer+str(EleDiffFlag)+spacer+str(DetLimFlag)+spacer+str(ErrorFlag)+spacer+str(LogPctFlag)+spacer+str(DLBlankFlag)+spacer+str(ErrBlankFlag)+spacer+str(Final))
PreBeam = "{:.3f}".format(float([s for s in d if '$XM_DATA_PROBE_CURRENT_PRE' in s][0][1])*1e9)
PostBeam = "{:.3f}".format(float([s for s in d if '$XM_DATA_PROBE_CURRENT_POST' in s][0][1])*1e9)
for fileGRD in glob.glob(os.path.join(path,'*_.grd')):
    print(fileGRD)
    wdsloc = re.sub("[]'[]",'',fileGRD.split('\\')[1]).find('WDS')
    ChanNum = re.sub("[]'[]",'',fileGRD.split('\\')[1])[wdsloc+3]
    fileGRDname = re.sub("[]'[]",'',fileGRD.split('\\')[1])
    fc.write('0'+spacer+str(ChanNum)+spacer+str(WDSDwell)+spacer+str(PreBeam)+spacer+str(PostBeam)+spacer+str(excelstore)+spacer+str(excelstore3)+spacer+'"'+fileGRDname+'"')
livefile = tkinter.filedialog.askopenfile(title="Select live time .csv file")
livedata = genfromtxt(livefile, delimiter=',')
EDSLive = np.median(livedata)
for fileGRD in glob.glob(os.path.join(path,'*EDS.grd')):
    print(fileGRD)
    ChanNum = 0
    fileGRDname = re.sub("[]'[]",'',fileGRD.split('\\')[1])
    fc.write('0'+spacer+str(ChanNum)+spacer+str(EDSLive)+spacer+str(PreBeam)+spacer+str(PostBeam)+spacer+str(excelstore)+spacer+str(excelstore3)+spacer+'"'+fileGRDname+'"')
for fileGRD in glob.glob(os.path.join(path,'*POFF.grd')):
    print(fileGRD)
    wdsloc = re.sub("[]'[]",'',fileGRD.split('\\')[1]).find('WDS')
    ChanNum = re.sub("[]'[]",'',fileGRD.split('\\')[1])[wdsloc+3]
    fileGRDname = re.sub("[]'[]",'',fileGRD.split('\\')[1])
    fc.write('1'+spacer+str(ChanNum)+spacer+str(WDSDwell)+spacer+str(PreBeam)+spacer+str(PostBeam)+spacer+str(excelstore)+spacer+str(excelstore3)+spacer+'"'+fileGRDname+'"')
for fileGRD in glob.glob(os.path.join(path,'*NOFF.grd')):
    print(fileGRD)
    wdsloc = re.sub("[]'[]",'',fileGRD.split('\\')[1]).find('WDS')
    ChanNum = re.sub("[]'[]",'',fileGRD.split('\\')[1])[wdsloc+3]
    fileGRDname = re.sub("[]'[]",'',fileGRD.split('\\')[1])
    fc.write('2'+spacer+str(ChanNum)+spacer+str(WDSDwell)+spacer+str(PreBeam)+spacer+str(PostBeam)+spacer+str(excelstore)+spacer+str(excelstore3)+spacer+'"'+fileGRDname+'"')
fc.write('10')
fc.write(' 0  0  0  0  0  0  0  0  0  0 ')
fc.write('0')
TitleAppendFlag = -1
SurferTemplateFlag = 0
SurferSliceTemplateFlag = 0
SurferPolyTemplateFlag = 0
SurferStripTemplateFlag = 0
SpareFlag1 = 0
SpareFlag2 = 0
fc.write(TitleAppendFlag+spacer+SurferTemplateFlag+spacer+SurferSliceTemplateFlag+spacer+SurferPolyTemplateFlag+spacer+SurferStripTemplateFlag+spacer+SpareFlag1+spacer+SpareFlag2)
#EDS spectrum image not utilized
SpecImageFlag = 0
fc.write(SpecImageFlag+spacer+'"'+'"')
ScanType = 0 #0=beam 1=stage
StagePolarity = 0 #0=cameca 1=jeol
fc.write(ScanType+spacer+StagePolarity)
fc.write('0'+spacer+'"'+'SE'+'"'+spacer+'0'+spacer+'"'+'BSE'+'"'+spacer+'0'+spacer+'"'+'CL'+'"')
for fileGRD in glob.glob(os.path.join(path,'*SEI.grd')):
    print(fileGRD)
    SEIname = re.sub("[]'[]",'',fileGRD.split('\\')[1])
for fileGRD in glob.glob(os.path.join(path,'*COMP.grd')):
    print(fileGRD)
    COMPname = re.sub("[]'[]",'',fileGRD.split('\\')[1])
fc.write(SEIname+spacer+COMPname+spacer+'"'+'"')
#tdi corrections
tdi_num = 0 #number of tdi maps
tdi_intervals = 0 #number of tdi intervals
fc.write(tdi_num+spacer+tdi_intervals)
#placeholder flags
fc.write(' 0             0             0             0             0             0 ')


[John Donovan]

Thanks for this post and the help file flag.

I'm just working through programming it in python.

I love this entry in the file definition, it made me smile

Code Select Expand

The next line contains flags for output of analog signal images:

0            "SE"          0            "BSE"          0            "CL"

"MSH4-1_00653_VS1.grd"      ""            ""

It's pretty self explanatory


What do the zeros mean in first line?

Sorry about that!   

The code from above is:

Code Select Expand

' If version 6, read analog signal image output flags and names
If CalcImageProjectVersion% >= 6 Then
Input #CalcImageProjectFileNumber%, CalcImageAnalogSignalFlags(1), CalcImageAnalogSignalLabels(1), CalcImageAnalogSignalFlags(2), CalcImageAnalogSignalLabels(2), CalcImageAnalogSignalFlags(3), CalcImageAnalogSignalLabels(3)
End If

The CalcImageAnalogSignalFlags parameters are booleans (0 or -1) and indicates if the image is to be displayed along with the x-ray maps as seen here in the GUI:

Second line is a list of the file names, does "" mean no file present

The code is:

Code Select Expand

' If version 7, read analog signal image filenames
If CalcImageProjectVersion% >= 7 Then
Input #CalcImageProjectFileNumber%, AnalogFilenames$(1), AnalogFilenames$(2), AnalogFilenames$(3)
If Trim$(AnalogFilenames$(1)) <> vbNullString Then AnalogFilenames$(1) = MiscGetPathOnly$(CalcImageProjectFile$) & AnalogFilenames$(1)
If Trim$(AnalogFilenames$(2)) <> vbNullString Then AnalogFilenames$(2) = MiscGetPathOnly$(CalcImageProjectFile$) & AnalogFilenames$(2)
If Trim$(AnalogFilenames$(3)) <> vbNullString Then AnalogFilenames$(3) = MiscGetPathOnly$(CalcImageProjectFile$) & AnalogFilenames$(3)
End If

So yes, an empty double quotes means no image file was specified.

[Ben Buse]

Great thanks

[Ben Buse]

Ok here's latest version of the code and the file generated attached

When I load the generated cip file in CalcImage, it says 'input past end of file' so I'm obviously missing something

Should each line have a leading zero?

And I see I've missed the dynamic element feature lines at the end, - I guess I need to add them.

Code Select Expand

#where only one set of maps in folder
#where uses last sample in mdb
#where mdb in same folder and only one mdb present
import tkinter
from tkinter import filedialog
import numpy as np
from numpy import genfromtxt
import csv
import datetime
import pyodbc
import glob
import re
import os
cndfile = tkinter.filedialog.askopenfile(title="Select WDS element .cnd file")
reader = csv.reader(open(cndfile.name), delimiter=" ")
d = list(reader)
ProjectName = ' '.join(d[29][1:len(d[29])])
path = filedialog.askdirectory(title="Select location of grd files")
fc = open(path + '/' + 'test cip creation.cip','w')
fc.write('12'+'          '+'"'+'CalcImage Quantitative Image Project'+' '+datetime.datetime.now().strftime("%x")+' '+datetime.datetime.now().strftime("%X")+'"'+'\n')
for fileMDB in glob.glob(os.path.join(path,'*.MDB')):
    print(fileMDB)
MDBname = re.sub("[]'[]",'',fileMDB.split('\\')[1]).split('.MDB')[0]
MDBfile = re.sub("[]'[]",'',fileMDB.split('\\')[1])
spacer = '            '
fc.write('"'+MDBname+'_'+ProjectName+'00001_'+'"'+'\n')
fc.write('"'+MDBfile+'"'+'\n')
MDB = fileMDB
DRV = 'Microsoft Access Driver (*.mdb, *.accdb)'
PWD = 'pw'
con = pyodbc.connect('DRIVER={};DBQ={};PWD={}'.format(DRV,MDB,PWD))
cur = con.cursor()
SQL = 'SELECT * FROM Sample;'
rows = cur.execute(SQL).fetchall()
LastSample = len(rows)
cur.close()
con.close()
MapCounter = len(glob.glob1(path,'*_.grd'))
MapCounterEDS = len(glob.glob1(path,'*EDS.grd'))
#MinusOxygen = 1
MapCounterPOFF = len(glob.glob1(path,'*POFF.grd'))
MapCounterNOFF = len(glob.glob1(path,'*NOFF.grd'))
#NumMaps = MapCounter+MapCounterEDS-MinusOxygen
NumMaps = MapCounter+MapCounterEDS+MapCounterPOFF+MapCounterNOFF
TotalsImageFlag = -1
StoicOxFlag = -1
ExcessOxFlag = 0
NetIntenFlag = 0
BgdIntenFlag = 0
KratioIntenFlag = 0
QuantPercFlag = -1
AtomPercFlag = 0
OxidePercFlag = -1
FormulaBasisFlag = 0
EleDiffFlag = 0
DetLimFlag = 0
ErrorFlag = 0
LogPctFlag = 0
DLBlankFlag = 0
ErrBlankFlag = 0
Final = 0
sub = '$XM_AP_SA_DWELL_TIME%0'
WDSDwell = [s for s in d if sub in s][0][1]
sub2 = '$XM_DATA_SAVE_DATE'
offset = 693594
#exceldate = datetime.datetime.date(datetime.datetime.strptime([s for s in d if sub2 in s][0][1],"%Y/%m/%d")).toordinal()-offset
exceltim = datetime.datetime(1899,12,30)
cnddatetime=[s for s in d if sub2 in s][0][1]+' '+[s for s in d if sub2 in s][0][2]
delta=datetime.datetime.strptime(cnddatetime,'%Y/%m/%d %H:%M:%S')-exceltim
excelstore = float(delta.days)+(float(delta.seconds)/86400)
sub3 = '$XM_CP_DATE'
cnddatetime3=[s for s in d if sub3 in s][0][1]+' '+[s for s in d if sub3 in s][0][2]
delta3=datetime.datetime.strptime(cnddatetime3,'%Y/%m/%d %H:%M:%S')-exceltim
excelstore3 = float(delta3.days)+(float(delta3.seconds)/86400)
fc.write(str(LastSample)+spacer+str(NumMaps)+spacer+str(TotalsImageFlag)+spacer+str(StoicOxFlag)+spacer+str(ExcessOxFlag)+spacer+str(NetIntenFlag)+spacer+str(BgdIntenFlag)+spacer+str(KratioIntenFlag)+spacer+str(QuantPercFlag)+spacer+str(AtomPercFlag)+spacer+str(OxidePercFlag)+spacer+str(FormulaBasisFlag)+spacer+str(EleDiffFlag)+spacer+str(DetLimFlag)+spacer+str(ErrorFlag)+spacer+str(LogPctFlag)+spacer+str(DLBlankFlag)+spacer+str(ErrBlankFlag)+spacer+str(Final)+'\n')
PreBeam = "{:.3f}".format(float([s for s in d if '$XM_DATA_PROBE_CURRENT_PRE' in s][0][1])*1e9)
PostBeam = "{:.3f}".format(float([s for s in d if '$XM_DATA_PROBE_CURRENT_POST' in s][0][1])*1e9)
for fileGRD in glob.glob(os.path.join(path,'*_.grd')):
    print(fileGRD)
    wdsloc = re.sub("[]'[]",'',fileGRD.split('\\')[1]).find('WDS')
    ChanNum = re.sub("[]'[]",'',fileGRD.split('\\')[1])[wdsloc+3]
    fileGRDname = re.sub("[]'[]",'',fileGRD.split('\\')[1])
    fc.write('0'+spacer+str(ChanNum)+spacer+str(WDSDwell)+spacer+str(PreBeam)+spacer+str(PostBeam)+spacer+str(excelstore)+spacer+str(excelstore3)+spacer+'"'+fileGRDname+'"'+'\n')
livefile = tkinter.filedialog.askopenfile(title="Select live time .csv file")
livedata = genfromtxt(livefile, delimiter=',')
EDSLive = np.median(livedata)
for fileGRD in glob.glob(os.path.join(path,'*EDS.grd')):
    print(fileGRD)
    ChanNum = 0
    fileGRDname = re.sub("[]'[]",'',fileGRD.split('\\')[1])
    fc.write('0'+spacer+str(ChanNum)+spacer+str(EDSLive)+spacer+str(PreBeam)+spacer+str(PostBeam)+spacer+str(excelstore)+spacer+str(excelstore3)+spacer+'"'+fileGRDname+'"'+'\n')
for fileGRD in glob.glob(os.path.join(path,'*POFF.grd')):
    print(fileGRD)
    wdsloc = re.sub("[]'[]",'',fileGRD.split('\\')[1]).find('WDS')
    ChanNum = re.sub("[]'[]",'',fileGRD.split('\\')[1])[wdsloc+3]
    fileGRDname = re.sub("[]'[]",'',fileGRD.split('\\')[1])
    fc.write('1'+spacer+str(ChanNum)+spacer+str(WDSDwell)+spacer+str(PreBeam)+spacer+str(PostBeam)+spacer+str(excelstore)+spacer+str(excelstore3)+spacer+'"'+fileGRDname+'"'+'\n')
for fileGRD in glob.glob(os.path.join(path,'*NOFF.grd')):
    print(fileGRD)
    wdsloc = re.sub("[]'[]",'',fileGRD.split('\\')[1]).find('WDS')
    ChanNum = re.sub("[]'[]",'',fileGRD.split('\\')[1])[wdsloc+3]
    fileGRDname = re.sub("[]'[]",'',fileGRD.split('\\')[1])
    fc.write('2'+spacer+str(ChanNum)+spacer+str(WDSDwell)+spacer+str(PreBeam)+spacer+str(PostBeam)+spacer+str(excelstore)+spacer+str(excelstore3)+spacer+'"'+fileGRDname+'"'+'\n')
fc.write('10'+'\n')
fc.write(' 0  0  0  0  0  0  0  0  0  0 '+'\n')
fc.write('0'+'\n')
TitleAppendFlag = -1
SurferTemplateFlag = 0
SurferSliceTemplateFlag = 0
SurferPolyTemplateFlag = 0
SurferStripTemplateFlag = 0
SpareFlag1 = 0
SpareFlag2 = 0
fc.write(str(TitleAppendFlag)+spacer+str(SurferTemplateFlag)+spacer+str(SurferSliceTemplateFlag)+spacer+str(SurferPolyTemplateFlag)+spacer+str(SurferStripTemplateFlag)+spacer+str(SpareFlag1)+spacer+str(SpareFlag2)+'\n')
#EDS spectrum image not utilized
SpecImageFlag = 0
fc.write(str(SpecImageFlag)+spacer+'"'+'"'+'\n')
#Could read scan type from cnd file. Are these flags used?
ScanType = 0 #0=beam 1=stage
StagePolarity = 0 #0=cameca 1=jeol
fc.write(str(ScanType)+spacer+str(StagePolarity)+'\n')
SEIflag = 0
COMPflag = 0
for fileGRD in glob.glob(os.path.join(path,'*SEI.grd')):
    print(fileGRD)
    SEIname = re.sub("[]'[]",'',fileGRD.split('\\')[1])
    SEIflag = 1
for fileGRD in glob.glob(os.path.join(path,'*COMP.grd')):
    print(fileGRD)
    COMPname = re.sub("[]'[]",'',fileGRD.split('\\')[1])
    COMPflag = 1
fc.write(str(SEIflag)+spacer+'"'+'SE'+'"'+spacer+str(COMPflag)+spacer+'"'+'BSE'+'"'+spacer+'0'+spacer+'"'+'CL'+'"'+'\n')
fc.write(SEIname+spacer+COMPname+spacer+'"'+'"'+'\n')
#tdi corrections
tdi_num = 0 #number of tdi maps
tdi_intervals = 0 #number of tdi intervals
fc.write(str(tdi_num)+spacer+str(tdi_intervals)+'\n')
#placeholder flags
fc.write(' 0            0            0            0            0            0 '+'\n')
fc.close()




[John Donovan]

When I load the generated cip file in CalcImage, it says 'input past end of file' so I'm obviously missing something

Yup, you'll need to add placeholders for dynamic elements.   The other approach is to edit the version number at the beginning of the CIP file to an earlier version number, and then CalcImage will automatically add these missing placeholders...

Should each line have a leading zero?

For the dynamic elements?  See the code and/or look at one of your own CIP files. Here's an example from one of my projects:

Code Select Expand

11           "CalcImage Quantitative Image Project 5/9/2023 9:32:09 AM"
"Sulfide_Interferences_04-15-2016_FeCu_Sulfide_00053_"
"Sulfide_Interferences_04-15-2016.MDB"
 12            15           -1             0             0             0             0             0            -1            -1             0             0             0            -1            -1             0             0             0             0
 0             7            1.000          99.7344       100.009       42475.8307291667            42476.03375  "FeCu_Sulfide_00053_SP1_Ca_PET_.grd"       0
 0             4            1.000          99.7344       100.009       42475.8307291667            42476.03375  "FeCu_Sulfide_00053_SP2_Mo_LPET_.grd"      0
 0             5            1.000          99.7344       100.009       42475.8307291667            42476.03375  "FeCu_Sulfide_00053_SP3_Zn_LLIF_.grd"      0
 0             2            1.000          99.7344       100.009       42475.8307291667            42476.03375  "FeCu_Sulfide_00053_SP4_S_PET_.grd"        0
 0             1            1.000          99.7344       100.009       42475.8307291667            42476.03375  "FeCu_Sulfide_00053_SP5_Fe_LIF_.grd"       0
 2             7            .500           100.101       100.177       42476.1366319444            42476.2391319444           "FeCu_Sulfide_00053_SP1_Ca_PET__MOFF.grd"  0
 1             7            .500           99.9938       100.116       42476.0338888889            42476.1364814815           "FeCu_Sulfide_00053_SP1_Ca_PET__POFF.grd"  0
 2             4            .500           100.101       100.177       42476.1366319444            42476.2391319444           "FeCu_Sulfide_00053_SP2_Mo_LPET__MOFF.grd"               0
 1             4            .500           99.9938       100.116       42476.0338888889            42476.1364814815           "FeCu_Sulfide_00053_SP2_Mo_LPET__POFF.grd"               0
 2             5            .500           100.101       100.177       42476.1366319444            42476.2391319444           "FeCu_Sulfide_00053_SP3_Zn_LLIF__MOFF.grd"               0
 1             5            .500           99.9938       100.116       42476.0338888889            42476.1364814815           "FeCu_Sulfide_00053_SP3_Zn_LLIF__POFF.grd"               0
 2             2            .500           100.101       100.177       42476.1366319444            42476.2391319444           "FeCu_Sulfide_00053_SP4_S_PET__MOFF.grd"   0
 1             2            .500           99.9938       100.116       42476.0338888889            42476.1364814815           "FeCu_Sulfide_00053_SP4_S_PET__POFF.grd"   0
 2             1            .500           100.101       100.177       42476.1366319444            42476.2391319444           "FeCu_Sulfide_00053_SP5_Fe_LIF__MOFF.grd"  0
 1             1            .500           99.9938       100.116       42476.0338888889            42476.1364814815           "FeCu_Sulfide_00053_SP5_Fe_LIF__POFF.grd"  0
 7
 0  0  0  0  0  0  0
 0
-1             0             0             0             0             0             0
 0            ""
 1             0
 0            "SE"           0            "BSE"          0            "CL"
""            ""            ""
 0             0
 0             0             0             0             0             0
 0
 1             0             0
 1             0             0
 1             0             0
 0             0
 0
 1             0             0
 1             0             0
 1             0             0
 0             0
 0
 1             0             0
 1             0             0
 1             0             0
 0             0
 0
 1             0             0
 1             0             0
 1             0             0
 0             0
 0
 1             0             0
 1             0             0
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[Ben Buse]

Thanks John,

Sorry another slip up, leading zeros should have read leading space.

I see from your example from line 4 onwards there is a leading space before first value in each line

[Ben Buse]

Sorry for another question what are the zeros after the map name, which are shown in your example but not in the help file

Code Select Expand

..."FeCu_Sulfide_00053_SP1_Ca_PET_.grd"      0As in this line

Code Select Expand

0             7            1.000          99.7344       100.009       42475.8307291667            42476.03375  "FeCu_Sulfide_00053_SP1_Ca_PET_.grd"       0

[John Donovan]

Sorry for another question what are the zeros after the map name, which are shown in your example but not in the help file

I had to look this up myself!  As shown in the code example here:

https://smf.probesoftware.com/index.php?topic=1844.msg14165#msg14165

it's for recording the spectrometer positions for performing multi-point background corrections in CalcImage:

https://smf.probesoftware.com/index.php?topic=249.msg12670#msg12670

https://smf.probesoftware.com/index.php?topic=510.msg12799#msg12799

These values are zero unless one is loading multiple background maps for use in the multi-point background correction as seen in Philip Poeml's CIP file:

Code Select Expand

12           "CalcImage Quantitative Image Project 6/8/2024 2:02:22 PM"
"SX60_analysis_SX60 #949 vertical large area_00853_"
"SX60_analysis.MDB"
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 0             7            .135           270.714       263.146       45399.9521296296            45401.2744328704           "SX60 #949 vertical large area_00853_WDS2_U_QTZ_.grd"    58210
 0             13           .135           270.714       263.146       45399.9521296296            45401.2744328704           "SX60 #949 vertical large area_00853_WDS3_Cs_LIF_.grd"   66705
 0             19           .135           270.714       263.146       45399.9521296296            45401.2744328704           "SX60 #949 vertical large area_00853_WDS4_Y_PET_.grd"    73838
 0             2            .135           259.773       255.15        45402.0083796296            45403.3304050926           "SX60 #949 vertical large area_00854_WDS1_La_LIF_.grd"   66203
 0             8            .135           259.773       255.15        45402.0083796296            45403.3304050926           "SX60 #949 vertical large area_00854_WDS2_Np_QTZ_.grd"   56604
 0             14           .135           259.773       255.15        45402.0083796296            45403.3304050926           "SX60 #949 vertical large area_00854_WDS3_Cr_LIF_.grd"   56917
 0             20           .135           259.773       255.15        45402.0083796296            45403.3304050926           "SX60 #949 vertical large area_00854_WDS4_Zr_PET_.grd"   69478
 0             3            .110           252.709       264.794       45403.6004050926            45404.6954398148           "SX60 #949 vertical large area_00855_WDS1_Ce_LIF_.grd"   63612
 0             9            .110           252.709       264.794       45403.6004050926            45404.6954398148           "SX60 #949 vertical large area_00855_WDS2_Pu_QTZ_.grd"   55064
 0             15           .110           252.709       264.794       45403.6004050926            45404.6954398148           "SX60 #949 vertical large area_00855_WDS3_Mn_LIF_.grd"   52252
 0             21           .110           252.709       264.794       45403.6004050926            45404.6954398148           "SX60 #949 vertical large area_00855_WDS4_Mo_PET_.grd"   61844
 0             4            .135           253.288       253.761       45404.9887037037            45406.3111111111           "SX60 #949 vertical large area_00856_WDS1_Pr_LIF_.grd"   61168
 0             10           .135           253.288       253.761       45404.9887037037            45406.3111111111           "SX60 #949 vertical large area_00856_WDS2_Am_QTZ_.grd"   53594
 0             16           .135           253.288       253.761       45404.9887037037            45406.3111111111           "SX60 #949 vertical large area_00856_WDS3_Gd_LIF_.grd"   50878
 0             22           .135           253.288       253.761       45404.9887037037            45406.3111111111           "SX60 #949 vertical large area_00856_WDS4_Ru_PET_.grd"   55405
 0             5            .160           247.291       252.297       45406.7075347222            45408.2500694444           "SX60 #949 vertical large area_00858_WDS1_Nd_LIF_.grd"   58866
 0             11           .160           247.291       252.297       45406.7075347222            45408.2500694444           "SX60 #949 vertical large area_00858_WDS2_Cm_QTZ_.grd"   49355
 0             17           .160           247.291       252.297       45406.7075347222            45408.2500694444           "SX60 #949 vertical large area_00858_WDS3_Fe_LIF_.grd"   48123
 0             23           .160           247.291       252.297       45406.7075347222            45408.2500694444           "SX60 #949 vertical large area_00858_WDS4_Rh_PET_.grd"   52551
 0             6            .150           251.259       252.388       45408.6489814815            45410.1065740741           "SX60 #949 vertical large area_00859_WDS1_Sm_LIF_.grd"   54627
 0             12           .150           251.259       252.388       45408.6489814815            45410.1065740741           "SX60 #949 vertical large area_00859_WDS2_Xe_QTZ_.grd"   44844
 0             18           .150           251.259       252.388       45408.6489814815            45410.1065740741           "SX60 #949 vertical large area_00859_WDS3_Ni_LIF_.grd"   41225
 0             24           .150           251.259       252.388       45408.6489814815            45410.1065740741           "SX60 #949 vertical large area_00859_WDS4_Pd_PET_.grd"   47370
 2             1            .030           259.911       259.636       45401.641400463             45402.0080902778           "SX60 #949 vertical large area_00853_WDS1_Ti_LIF__MOFF.grd"            60314
 1             1            .030           262.932       260.14        45401.2746296296            45401.6411921296           "SX60 #949 vertical large area_00853_WDS1_Ti_LIF__POFF.grd"            69365
 2             7            .030           259.911       259.636       45401.641400463             45402.0080902778           "SX60 #949 vertical large area_00853_WDS2_U_QTZ__MOFF.grd"             66128
 1             7            .030           262.932       260.14        45401.2746296296            45401.6411921296           "SX60 #949 vertical large area_00853_WDS2_U_QTZ__POFF.grd"             66282
 2             13           .030           259.911       259.636       45401.641400463             45402.0080902778           "SX60 #949 vertical large area_00853_WDS3_Cs_LIF__MOFF.grd"            57943
 1             13           .030           262.932       260.14        45401.2746296296            45401.6411921296           "SX60 #949 vertical large area_00853_WDS3_Cs_LIF__POFF.grd"            67288
 2             19           .030           259.911       259.636       45401.641400463             45402.0080902778           "SX60 #949 vertical large area_00853_WDS4_Y_PET__MOFF.grd"             63480
 1             19           .030           262.932       260.14        45401.2746296296            45401.6411921296           "SX60 #949 vertical large area_00853_WDS4_Y_PET__POFF.grd"             75033
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 2             24           .030           254.112       255.302       45410.4760069444            45410.8446875              "SX60 #949 vertical large area_00859_WDS4_Pd_PET__MOFF.grd"            45360
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"SX60 #949 vertical large area_00858_VS1.grd"           "SX60 #949 vertical large area_00859_VS2.grd"           ""
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