Update loading of .topostats now just data is returned

[ns-rse]

In light of changing what [AFMReader returns](AFM-SPM/AFMReader#112** so that _just** the data is
returned we will need to update TopoStats to handle this.

IMPORTANT This will require co-ordination with AFMReader releases with clear advice to update to newer versions of
AFMReader and pip install --no-cache-dir --upgrade topostats.

Points that need changing....

io.py

LoadScans.load_topostats()

Line 679

            image, px_to_nm_scaling, data = topostats.load_topostats(self.img_path)

...will be...

            data = topostats.load_topostats(self.img_path)

We then have a section that was introduced to handle whether we wanted different components starting on Line
683

        try:
            # We want everything if performing any step beyond filtering (or explicitly ask for None/"all")
            if extract in [None, "all", "grains", "grainstats"]:
                return (image, px_to_nm_scaling, data)
            # Otherwise we want the raw/image_original
            if extract == "filter":
                return (image, px_to_nm_scaling, None)
            return (data[map_stage_to_image[extract]], px_to_nm_scaling, None)
        except KeyError as ke:
            raise KeyError(f"Can not extract array of type '{extract}' from .topostats objects.") from ke

...as we will only ever be returning data this can be replaced with

        return data

LoadScans.get_data()

There are a logical checks here that may need changing to account for only receiving data. This section extracts
self.image selt.pixel_to_nm_scaling and optionally data depending on the type of processing being undertaken. This
is stored in the self.extract and represents all or the stage (e.g. filter, grain, grainstats).

A key point which I missed when working on this was that the else: after the try: ... except: ... as I forgot that
the else: will run if no exception is raised (i.e. try: is successful), and this step builds a dictionary of the
images/data.

Line 782

                try:
                    if suffix == ".topostats" and self.extract in (None, "all", "grains", "grainstats"):
                        self.image, self.pixel_to_nm_scaling, data = self.load_topostats()
                    elif suffix == ".topostats" and self.extract not in (None, "all"):
                        self.image, self.pixel_to_nm_scaling, _ = self.load_topostats(self.extract)
                    else:
                        self.image, self.pixel_to_nm_scaling = suffix_to_loader[suffix]()
                except Exception as e:
                    if "Channel" in str(e) and "not found" in str(e):
                        LOGGER.warning(e)  # log the specific error message
                        LOGGER.warning(f"[{self.filename}] Channel {self.channel} not found, skipping image.")
                    else:
                        raise
                else:
                    if suffix == ".asd":
                        for index, frame in enumerate(self.image):
                            self._check_image_size_and_add_to_dict(image=frame, filename=f"{self.filename}_{index}")
                    # If we have extracted the image dictionary (only possible with .topostats files) we add that to the
                    # dictionary
                    elif data is not None:
                        data["img_path"] = img_path.with_suffix("")
                        self.img_dict[self.filename] = self.clean_dict(img_dict=data)
                    # Otherwise check the size and add image to dictionary
                    else:
                        self._check_image_size_and_add_to_dict(image=self.image, filename=self.filename)

Could probably be

                try:
                    if suffix == ".topostats":
                        data = self.load_topostats()
                        self.image = data["image"]
                        self.pixel_to_nm_scaling = data["pixel_to_nm_scaling"]
                    else:
                        self.image, self.pixel_to_nm_scaling = suffix_to_loader[suffix]()
                except Exception as e:
                    if "Channel" in str(e) and "not found" in str(e):
                        LOGGER.warning(e)  # log the specific error message
                        LOGGER.warning(f"[{self.filename}] Channel {self.channel} not found, skipping image.")
                    else:
                        raise
                else:
                    if suffix == ".asd":
                        for index, frame in enumerate(self.image):
                            self._check_image_size_and_add_to_dict(image=frame, filename=f"{self.filename}_{index}")
                    # If we have extracted the image dictionary (only possible with .topostats files) we add that to the
                    # dictionary
                    elif data is not None:
                        data["img_path"] = img_path.with_suffix("")
                        self.img_dict[self.filename] = self.clean_dict(img_dict=data)
                    # Otherwise check the size and add image to dictionary
                    else:
                        self._check_image_size_and_add_to_dict(image=self.image, filename=self.filename)

run_modules.py

The entry points/functions for running topostats {filters|grains} shouldn't need changing I don't think but worth
noting this is where the returned data is used. Something in the back of my mind says they will need changing but I
can't see it right now, perhaps it will be the process_filters() as this will have to extract the original_image from
the returned data as it will no longer be receiving a dictionary with this as the first item. Probably similar for the
process() function too, but I think the process_grains() function will be ok as its expecting to get a dictionary.