Bart, thank you for this valuable tool.
If you don't mind, I have a few questions related to macro photography,
1) Aperture: Should I use the equivalent aperture (adjusted for magnification) or the lens uncorrected aperture?
2) Focal length: in lenses with internal focusing, does it matter if the focal length varies at close range? Should I consider the adjusted focal length?
3) Can you recommend a procedure to determine pupil factor?
4) Focus stacking: are the steps the same regardless of the method to change focus between images? (Focus lens, change camera+lens position or moving the back only when using a bellows)
Great questions! Hope you like the answers
1) You use the regular Aperture that you've dialed in on the camera/lens. The equivalent aperture or effective aperture as it is called by some, is used to allow for an adjustment of the exposure time due to added lens extension.
Because the correction is usually executed by lengthening the exposure time, and not by opening up the aperture (which changes DOF), I've avoided mentioning 'effective aperture'. It tends to confuse, although many use it..
I make a separate mention of the effect on exposure in the comment behind 2.6.1), where both the (required) extension compared to infinity focus is mentioned, as well as the 'bellows factor' or required additional exposure. I've changed the latter from a simple multiplication factor to the number of EVs ('stops') that is required to achieve correct exposure, when it's not measured through the lens. That is mostly used to correct external light measuring and flashes, which cannot know how much extension was applied to achieve the required magnification. On flashes the power can often also be regulated by fixed (1/3rd, or other fractions of) EV amounts, or they are coupled automatically with the lightmetering system which measures through the lens.
2) We have no way of knowing the actual focal length, especially with Macro lenses with internal focusing groups of elements. They may reduce the focal length to allow closer focusing without the need for a longer lens tube/barrel. Therefore, the only result we can measure with certainty is the image magnification. That is also the most common way of dealing with macro issues. I know my EF 100mm f/2.8 II Macro uses internal focusing and extension, and my MP-E 65mm uses primarily, if not exclusively, extension.
So, whether the focal length is reduced, or the extension is effectively increased, we don't know, but the magnification is what will cause the exposure extension and the magnification of the blur/COC and diffraction effects. So in the end, it shouldn't matter much if the extension or the focal length changes, or both, as long as we know the magnification factor. It's usually indicated on a dedicated Macro lens, or simple to measure by focusing on something with known dimensions, such as a ruler or a coin, and compare that to the captured percentage of the sensor/film dimensions.
In Photomacrography, it is not reliable to measure it from the Focus distance used in lens formulae, including my tool, because we don't know the exact optical design and where that positions the optical primary and secondary principle planes.
So my recommendation is, enter the manufacturer's suggested focal length, and use the magnification factor to take care of all other effects.
3) The only procedure that's simple to execute is to look through the lens when not attached to the body, in front of a bright background. Hold it at arm's length and hold a ruler near the side facing you and measure the apparent diameter of the aperture. You measure the entrance pupil with the front of the lens facing you, and the exit pupil with that end of the lens facing you. The Exit (rear) diameter divided by the Entrance (front) diameter is the Pupil factor. It may, or may not, make some difference if the lens is focused at anything else than infinity, due to the internal focusing.
4) There is a difference between using (internal) lens focusing, which follows the magnification rules of my tool as you change the focus distance, and stepping the camera and lens together in a fixed setting on a focus rail. When focusing with the lens, one will need to use progressively larger steps as distance increases, or use the narrowest DOF zone and step through the scene with that (but that will require more slices than strictly needed).
When the focus rail method is used, which I prefer when things get really magnified a lot, like with the MP-E 65mm, then the magnification factor is also unchanged, and the DOF slice will be constant. So in that situation you just calculate the DOF of a given magnification factor, and use that as your fixed step increment.
There is another difference between the two methods, and that has to do with the amount of distance change of the entrance pupil relative to the subject. When the entrance pupil changes position, as is usually the case unless we use equipment which allow to only change the sensor plane position, the perspective changes as well. Dedicated stacking software will compensate by changing the slice magnification, but cannot deal with some of the occlusion effects and perspective shifts between foreground and background features. So, unless the DOF is extremely shallow, there may be stacking errors. Rik Littlefield has written an excellent article
So, whenever lens focusing is used to step through the DOF zones, you can use my tool for guidance on step size and number of required steps, and when a focus rail is used with a fixed magnification factor, you can use my tool to determine that fixed DOF zone depth. It will be difficult to focus by measuring focus distance, because it is not obvious from where on the lens itself to measure, so some common sense needs to be applied, or the shallowest DOF slice distance should be used for all slices. It's better to have no gaps in a focus stack, so I'd err on the side of caution.