Converting PDF/A to PDF while combining images

Thanks in advance for your assistance!
I have a quantity of PDF/A that I need to convert to standard PDFs. However, here's the wrinkle: each file has separate images that are layered over each other. I really need one image that has all the separate images combined. Further information: there's embedded text that needs to be preserved. An example image is here. An example of what it needs to look like is here.
How do I do this in Acrobat Pro XI? I've tried a bunch of different things but had no success. I was hoping someone with more experience has some suggestions. Thanks!

Well, the situation is this. We have an OCR program that reads tiffs of historic newspapers and makes PDFs of them. Then we have another piece of software that creates an XML (containing the text and related metadata) and PNG for screen display using the PDF as the source. Then these are ingested into a third software package that makes the newspaper pages searchable and displays the PNG via the web. It then offers the PDF as a download.
This works for us BUT we upgraded the OCR program and accidentally changed from PDF to PDF/A. For whatever reason the PDFs output with a single image but PDF/A takes any pictures or drawings and makes the separate image layers while "cutting" the pictures out of the main image. The software that creates the XML can only process the first image it finds in the PDF. We didn't detect the change until we had OCRed about 30,000 pages.
We unfortunately pay per page for the OCRing. So I'm hoping to fix the incorrect files rather than going back and re-OCRing the whole batch and have to pay again on the same pages. We corrected the process and now PDFs come out of the OCR with just one image. So moving forward we're fine.
So that's why I'm trying to find a way to flatten the images.

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Combining images to PDF in folder based on prefix

I have an arbitary folder with images in them, that are named like this:
00_01.tiff
00_02.tiff
00_03.tiff
00_03.tiff
01.tiff
02-1_01.tiff
02-1_02.tiff
02-2_01.tiff
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In short the rule would be:
if text 3 in fileName = "_" then
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else
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end if
It is easy to combine files to PDF's with Automator, but introducing this logic and doing the combining in Applescript is out of my league.
Does anybody have some suggestions on how I should go about solving this?
Best regards,
Knut

Jacques Rioux wrote:
Does the script should search in the subfolders?
No, I did not intend it to search through subfolders. I have thought about maybe first putting each group of files in to subfolders, and then iterate through the folders and do the PDF conversion then. That would be quite close to what the script you wrote is doing. More about that at the end of this reply.
Do you have multiple image formats (the name extension) to find in the source folder or in subfolders?
No, there will only ever be .tiff images in the folder. The contents of the folder is created by another script (as a part of a bigger workflow).
Do you have any PDF documents or PDF images to find in the source folder or in subfolders that you want to combine?
No, there will only be images in .tiff format. I mistyped in my previous post - it should have said .tiff there too, and not .pdf. Sorry about that.
xx.tif and xx_y.tif : Is it the number in xx can be the same or always different?
If the answer is not always different, (11.tiff and 11_2.tiff) Does the script should create one PDF or two PDF?
If the answer is two PDF, how do you rename the new PDF file? --> (11.pdf and 11_2.pdf) both must be renamed "11.pdf"
I will remove the xx.tiff as a possibility. We will only have xx_yy.tiff or xx-z_yy.tiff to care about, and not xx.tiff.
I will give you some background information, maybe it is easier when understanding the use case. You can skip to the table below if this is not relevant. The reason for this naming convention, is so that yet another script can finalize the workflow later, when doing renaming based on the output name of the created PDF-file. My workflow is for digital archiving of sheet music.
The entire workflow is like this:
Scanning the sheet music.
Converting pdf-files to tiff.
Cleaning, straigthening and convert from grayscale to b/w with ScanTailor
Rename output files to the naming scheme I describe.
Convert the tiff images to pdf, per part. (this is the part I'm asking about here)
Renaming all the files to fit the archiving scheme.
Grouping and sorting the files, and creating zip-archives.
Archiving the entire digital copy of the set in our digital archive.
For our case, we're only interested in item 5 in the list. Another series of scripts and Automator workflows take care of the rest.
Each music piece consists of several parts.
In the filing system I have created, each part has a prefix with the xx-number, like this:
00 = Score
01 = Soprano cornet
02 = Solo cornet
17 = BbBass
18 = Percussion
The final files will have a name like (only an example):
02_SoloCn_31_SilentNight_Gordon.pdf
For some pieces there are more than one solo cornet part. That's why we get the z-component, to differentiate between the parts:
02-1 = Solo cornet 1 --> will get filename 02_SoloCn1_31_SilentNight_Gordon.pdf
02-2 = Solo cornet 2 --> will get filename 02_SoloCn2_31_SilentNight_Gordon.pdf
Many pieces has more than one page per part. That is where the yy component of the file name comes in, the only reason for the yy component is to keep all the pages in the correct order to make it easy to combine them programatically:
02-1_10.tiff = Solo cornet 1, page 1
02-1_11.tiff = Solo cornet 1, page 2
02-1_12.tiff = Solo cornet 1, page 3
Here is a table with the pattern, example of a possible filename and what the output pdf should be called:
Pattern
Example file name
Output pdf
xx_yy.tiff
01_10.tiff
01_11.tiff
01_12.tiff
01_13.tiff
01.pdf
xx_yy.tiff
12_10.tiff
12_11.tiff
12_12.tiff
12.pdf
xx-z_yy.tiff
02-1_10.tiff
02-1_11.tiff
02-1_12.tiff
02-1.pdf
xx-z_yy.tiff
02-2_10.tiff
02-2_11.tiff
02-2_12.tiff
02-2.pdf
Is it possible that there would be other characters after the pattern? --> example: 33_2test.tiff, 40-4_99ball.tiff
No, all the files will have just the components described above in the file name. No need for exception handling, since this is a tightly controlled workflow.
As i mentioned earlier in this reply, I have played with the thought of first running a script to sort all the files for one part into a subfolder with the correct name.
This I can do with the following script (I guess it would be more efficient with shell script or using System Event to do the moving):
          tell application "Finder"
set thisfolder to (choose folder)
set mylist to every file in thisfolder as alias list
repeat with eachfile in mylist
set filename to name of eachfile
if (character 3 of filename is "-") then
set prefix to characters 1 thru 4 of filename as text
else
set prefix to characters 1 thru 2 of filename as text
end if
try
set newfolder to ((thisfolder as text) & prefix) as alias
on error -- file not found
set newfolder to make new folder at thisfolder with properties {name:prefix}
end try
move eachfile to newfolder
end repeat
   end tell
After this, all the files have moved to folders with the folder name corresponding to the part number, like this:
01/01_10.tiff
01/01_11.tiff
02-1/02-1_10.tiff
02-1/02-1_11.tiff
and so on...
It would perhaps be easier to extend on this script, or create a new one, that will iterate each subfolder in a folder, and run the Automator action for combining images to files with each iteration?
What do you think? I'm sorry if this was too much information. Do not hesitate to ask if something is unclear (I bet it is!).
I really appreciate your help, Jacques!
Knut

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Could you please let me know what version of Acrobat are you using.
Also, tell me your workflow of combining those PDF files?
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thanks...figured out my problem!
Date: Wed, 3 Feb 2010 12:24:29 -0700
From: [email protected]
To: [email protected]
Subject: Re: After 9.3 update getting error printing to Adobe PDF while converting from Powerpoint to PDF
What happens if you try to print to the Adobe PDF printer?
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Converting PDF/A to PDF while combining images

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