I have frequently encountered a need to do the same thing. An example is a complex notebook which loads an image and analyzes it as scientific data. I want to run the same analysis on a large number of images to obtain a result for each. But the notebook is long and complex. Trying to merge it into a single cell for a function definition makes it almost unreadable and extremely difficult to debug when something breaks the analysis method.
My solution is to leave the analysis algorithm in the original notebook and call that notebook from a controlling notebook.
Here is how I do that:
The analysis notebook leads with a definition that defines the file name of the image to be analyzed. This notebook can be evaluated as a standalone notebook in development or later in debugging.
When I am satisfied that the analysis notebook is working correctly, I save a version in which the image file name is not defined, by just commenting out the leading definition.
I then create a controlling notebook which is usually very simple. It often runs a loop (or uses Map) to analyze a large number of images and saves the result for each. To do this it opens the analysis notebook and obtains a handle to it using, for example:
nb = NotebookOpen["AnalysisNotebook.nb"]
It now relies on the fact that the controlling notebook and the newly opened analysis notebook share the same kernel and therefore the same symbol definitions. It can run a loop like this:
Define an image file name using the symbol name used in the analysis notebook.
NotebookEvaluate[nb] to run the analysis.
Save the results which have been produced as symbol definitions by the analysis notebook. Often saved in a Dataset or just appended to a list.
Define a new image filename and do it again until done.
I wrote this as though it was done in a loop, but all of this can just be done by a function in the controlling notebook that is mapped onto a list of image file names.
I find this works really well. If some image breaks the analysis algorithm. I just open the analysis notebook, uncomment the leading definition and revise it to point to the offending image. Then execute the notebook a cell at a time in the usual way to locate the problem.
.wlfile, run it with
Get, and pass data to it through certain variables. $\endgroup$