diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py index 21a541ac..2c9f1913 100644 --- a/src/openflexure_microscope_server/things/smart_scan.py +++ b/src/openflexure_microscope_server/things/smart_scan.py @@ -203,6 +203,9 @@ class SmartScanThing(Thing): try: self._check_background_and_csm_set() self._ongoing_scan_name = self._get_unique_scan_name_and_dir(scan_name) + self.create_zip_of_scan( + logger=self._scan_logger, scan_name=self._ongoing_scan_name + ) self._autofocus.looping_autofocus(dz=self.autofocus_dz, start="centre") # record starting position so we can return there self._starting_position = self._stage.position @@ -232,6 +235,30 @@ class SmartScanThing(Thing): self._scan_data = None self._scan_lock.release() + def promote_stitch_files( + self, + logger, + ): + """Copy the stitched image from the scan images folder to the top level""" + + # Search the scan images dir for a file ending in '_stitched.jpg + stitched_image_path = glob.glob( + os.path.join(self._ongoing_scan_images_dir, "*_stitched.jpg") + ) + + if len(stitched_image_path) == 0: + logger.warning("Could't find a stitched image to copy") + else: + for stitched_image in stitched_image_path: + stitch_name = os.path.basename(stitched_image) + + shutil.copy( + stitched_image, + os.path.join( + self.dir_for_scan(self._ongoing_scan_name), stitch_name + ), + ) + @_scan_running def _check_background_and_csm_set(self): """Before starting a scan check that background and camera-stage-mapping are set @@ -597,10 +624,8 @@ class SmartScanThing(Thing): # increment capure counter as thread has completed self._scan_images_taken += 1 # Add it to the incremental zip - self.create_zip_of_scan( - logger=self._scan_logger, + self.update_zip( scan_name=self._ongoing_scan_name, - download_zip=False, ) @_scan_running @@ -655,10 +680,9 @@ class SmartScanThing(Thing): self._scan_logger.info("Not performing a stitch as 3 or fewer images taken") return - self.create_zip_of_scan( - logger=self._scan_logger, + self.update_zip( scan_name=self._ongoing_scan_name, - download_zip=False, + final_version=False, ) self._scan_logger.info("Waiting for background processes to finish...") @@ -671,6 +695,7 @@ class SmartScanThing(Thing): scan_name=self._ongoing_scan_name, overlap=self._scan_data["overlap"], ) + self.promote_stitch_files(self._scan_logger) except SubprocessError as e: self._scan_logger.error(f"Stitching failed: {e}", exc_info=e) @@ -1044,13 +1069,8 @@ class SmartScanThing(Thing): self, logger: InvocationLogger, scan_name: str, - download_zip=True, - ) -> ZipBlob: - """Generate a zip file that can be downloaded, with all the scan files in it. - - Note that as this is a thing_action it needs the logger passed as - a variable if called from another thing action - """ + ) -> None: + """Generate an empty zip file for the current scan""" images_folder = self.images_dir_for_scan(scan_name=scan_name) scan_folder = self.dir_for_scan(scan_name=scan_name) @@ -1062,12 +1082,25 @@ class SmartScanThing(Thing): zip_fname = os.path.join(scan_folder, "images.zip") # Create an empty zip file - we don't want to autofill it with files, - # as some of them should only be added at the end (as we can't overwrite) + # as some of them should only be added at the end, as we can't overwrite # them once they change if not os.path.isfile(zip_fname): - with zipfile.ZipFile(zip_fname, mode="w") as scan_zip: + with zipfile.ZipFile(zip_fname, mode="w"): pass + def update_zip( + self, + scan_name: str, + final_version: bool = False, + ) -> None: + """Update the zip file with any images added to the folder since the last run, + except for files containing 'files_to_delay', which are files to only include + once the scan is finished or the user wants to download the zip + """ + scan_folder = self.dir_for_scan(scan_name=scan_name) + + zip_fname = os.path.join(scan_folder, "images.zip") + # get a list of files in the existing zip current_zip = self.get_files_in_zip(zip_fname) @@ -1085,43 +1118,46 @@ class SmartScanThing(Thing): "stitched.jp", "stitched_from", "stitched.om", + "stitching_correlations", ] - tiff_name = "" with zipfile.ZipFile(zip_fname, mode="a") as scan_zip: for file in files: - if "stitched.jp" in file: - stitch_name = os.path.split(file)[1] - if ".ome.tiff" in file: - tiff_name = os.path.split(file)[1] - if any(banned_name in file for banned_name in files_to_delay): + if any(skipped_name in file for skipped_name in files_to_delay): pass elif file in current_zip: pass - elif ".zip" in file or "raw" in file: + elif ".zip" in file: pass else: - logger.info(f"appending {file} to zip") scan_zip.write(os.path.join(scan_folder, file), arcname=file) - # Promote key files to the top level of the zip only at the end of the scan (when downloading) - # and finally zip some of the final files + # Finally zip the updating files we skipped previously # TODO: if you download multiple times, you get duplicate files - is this a problem? - if download_zip: + # TODO: check if they're already in + if final_version: with zipfile.ZipFile(zip_fname, mode="a") as scan_zip: - for fname in ["stitched_from_stage.jpg", stitch_name, tiff_name]: - fpath = os.path.join(images_folder, fname) - if os.path.exists(fpath): - logger.info(f"copying {fpath} to upper level") - scan_zip.write(fpath, arcname=fname) for file in files: - if any(banned_name in file for banned_name in files_to_delay): - logger.info(f"we are finally adding {file} into zip") + if any(delayed_name in file for delayed_name in files_to_delay): scan_zip.write(os.path.join(scan_folder, file), arcname=file) - logger.info("about to download zip") - return ZipBlob.from_file(zip_fname) @thing_action + def download_zip( + self, + scan_name: str, + ): + """Update the zip to include the files we leave to the end, then return the + zip file as a Blob""" + self.update_zip( + scan_name=scan_name, + final_version=True, + ) + + scan_folder = self.dir_for_scan(scan_name=scan_name) + + zip_fname = os.path.join(scan_folder, "images.zip") + return ZipBlob.from_file(zip_fname) + def get_files_in_zip(self, zip_path): """List the relative paths of all files and folders in the zip folder specified""" scan_zip = zipfile.ZipFile(zip_path) diff --git a/webapp/src/components/tabContentComponents/scanListContent.vue b/webapp/src/components/tabContentComponents/scanListContent.vue index 7bbb4a8a..3d018826 100644 --- a/webapp/src/components/tabContentComponents/scanListContent.vue +++ b/webapp/src/components/tabContentComponents/scanListContent.vue @@ -68,7 +68,7 @@

{{ item.name }}