From 62065dc385f192869adaa00e9e163f9137f97322 Mon Sep 17 00:00:00 2001
From: jaknapper <jaknapper@hotmail.com>
Date: Tue, 24 Jun 2025 18:02:11 +0100
Subject: [PATCH 01/12] Add download stitch button to GUI

---
 .../tabContentComponents/scanListContent.vue     | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/webapp/src/components/tabContentComponents/scanListContent.vue b/webapp/src/components/tabContentComponents/scanListContent.vue
index 79741558..db60cc20 100644
--- a/webapp/src/components/tabContentComponents/scanListContent.vue
+++ b/webapp/src/components/tabContentComponents/scanListContent.vue
@@ -89,13 +89,25 @@
                 <action-button
                 thing="smart_scan"
                 action="download_zip"
-                submit-label="Download ZIP"
+                submit-label="Download All"
                 :can-terminate="false"
                 :submit-data="{ scan_name: item.name }"
                 :button-primary="true"
                 @response="downloadZipFile"
                 @error="modalError"
-              />
+                class="uk-button uk-width-1-2"
+                />
+                <action-button
+                thing="smart_scan"
+                action="download_zip"
+                submit-label="Download Stitch"
+                :can-terminate="false"
+                :submit-data="{ scan_name: item.name }"
+                :button-primary="true"
+                @response="downloadZipFile"
+                @error="modalError"
+                class="uk-button uk-width-1-2"
+                />
               <button
                 class="uk-button uk-button-default uk-width-1-1"
                 @click="deleteScan(item.name)"

From ff43deae368e98a0a9037d7262c0b05127497e1e Mon Sep 17 00:00:00 2001
From: jaknapper <jaknapper@hotmail.com>
Date: Wed, 25 Jun 2025 14:34:24 +0100
Subject: [PATCH 02/12] Download stitched image of scan (if present)

* Docstring for download stitch
* use global STITCH_SUFFIX
---
 .../scan_directories.py                       | 66 +++++++++++++++----
 .../things/smart_scan.py                      | 24 +++++++
 .../tabContentComponents/scanListContent.vue  | 26 ++++----
 3 files changed, 91 insertions(+), 25 deletions(-)

diff --git a/src/openflexure_microscope_server/scan_directories.py b/src/openflexure_microscope_server/scan_directories.py
index e2a33fbc..76fe0185 100644
--- a/src/openflexure_microscope_server/scan_directories.py
+++ b/src/openflexure_microscope_server/scan_directories.py
@@ -5,7 +5,7 @@ Currently it handles scan getting information from a information from a scan dir
 eventually is should handle all the file system operation for smart_scan.
 """
 
-from typing import Optional
+from typing import Optional, Literal
 import os
 import re
 import shutil
@@ -13,6 +13,7 @@ import zipfile
 
 from pydantic import BaseModel
 
+STITCH_SUFFIX = "_stitched.jpg"
 IMG_DIR_NAME = "images"
 IMAGE_REGEX = re.compile(r"-?[0-9]+_-?[0-9]+\.jpe?g$")
 SCAN_ZERO_PAD_DIGITS = 4
@@ -88,7 +89,7 @@ class ScanDirectoryManager:
         """Return the file path for the file within a scan directory
 
         If check_exists is True, None is returned if the file does not exist. If False
-        then the path is returned anway
+        then the path is returned anyway
         """
         file_path = os.path.join(self.img_dir_for(scan_name), filename)
         if check_exists:
@@ -96,6 +97,13 @@ class ScanDirectoryManager:
                 return None
         return file_path
 
+    def get_final_stitch(self, scan_name: str) -> Optional[str]:
+        """Return the file path for the final stitch.
+
+        If no final stitch is found, return None
+        """
+        return ScanDirectory(scan_name, self.base_dir).get_final_stitch()
+
     @property
     def all_scans(self) -> list[str]:
         """Return a list of the scan names in the base directory"""
@@ -242,25 +250,55 @@ class ScanDirectory:
             return []
         return os.listdir(self.images_dir)
 
+    def _find_files(
+        self, file_types=Literal["all", "scan_images", "stitches", "dzi"]
+    ) -> tuple[list[str], list[str], list[str]] | list[str]:
+        folder_contents = self.get_scan_files()
+
+        # Return empty lists if no folder contents.
+        if not folder_contents:
+            if file_types == "all":
+                return [], [], []
+            return []
+
+        if file_types in ["all", "scan_images"]:
+            scan_images = [i for i in folder_contents if IMAGE_REGEX.search(i)]
+            if file_types == "scan_images":
+                return scan_images
+
+        if file_types in ["all", "stitches"]:
+            stitches = [i for i in folder_contents if i.endswith("_stitched.jpg")]
+            if file_types == "stitches":
+                return stitches
+
+        if file_types in ["all", "dzi"]:
+            dzi_files = [i for i in folder_contents if i.endswith("dzi")]
+            if file_types == "dzi":
+                return dzi_files
+
+        return scan_images, stitches, dzi_files
+
+    def get_final_stitch(self) -> Optional[str]:
+        """Return the file path for the final stitch.
+
+        If no final stitch is found, return None
+        """
+        stitches = self._find_files("stitches")
+        if not stitches:
+            return None
+        return stitches[0]
+
     def get_modified_time(self) -> float:
         """Return the modified time of the directory"""
         return max(os.stat(root).st_mtime for root, _, _ in os.walk(self.dir_path))
 
     def scan_info(self):
         """Return the information for the scan directory as a ScanInfo object"""
-        folder_contents = self.get_scan_files()
-        if folder_contents:
-            scan_images = [i for i in folder_contents if IMAGE_REGEX.search(i)]
-            stitches = [i for i in folder_contents if i.endswith("_stitched.jpg")]
-            dzi_files = [i for i in folder_contents if i.endswith("dzi")]
 
-            number_of_images = len(scan_images)
-            stitch_available = len(stitches) > 0
-            dzi = None if not dzi_files else str(dzi_files[0])
-        else:
-            number_of_images = 0
-            stitch_available = False
-            dzi = None
+        scan_images, stitches, dzi_files = self._find_files("all")
+        number_of_images = len(scan_images)
+        stitch_available = len(stitches) > 0
+        dzi = None if not dzi_files else str(dzi_files[0])
 
         return ScanInfo(
             name=self.name,
diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py
index 832f6170..36e73273 100644
--- a/src/openflexure_microscope_server/things/smart_scan.py
+++ b/src/openflexure_microscope_server/things/smart_scan.py
@@ -666,6 +666,30 @@ class SmartScanThing(Thing):
         """
         return self._scan_dir_manager.all_scans_info()
 
+    @fastapi_endpoint(
+        "get",
+        "get_stitch/{scan_name}",
+        responses={
+            200: {
+                "description": "Successfully downloading file",
+                "content": {"*/*": {}},
+            },
+            403: {"description": "Filename not permitted"},
+            404: {"description": "File not found"},
+        },
+    )
+    def get_stitch_file(self, scan_name: str) -> FileResponse:
+        """Return the stitched image corresponding to a given scan name, if it exists.
+
+        Will only return a file ending in suffix STITCH_SUFFIX
+        Note: when downloading this, the default filename will be `scan_name`.jpeg"""
+
+        stitch_path = self._scan_dir_manager.get_final_stitch(scan_name)
+
+        if stitch_path is None:
+            raise HTTPException(404, "File not found")
+        return FileResponse(stitch_path)
+
     @fastapi_endpoint(
         "delete",
         "scans/{scan_name}",
diff --git a/webapp/src/components/tabContentComponents/scanListContent.vue b/webapp/src/components/tabContentComponents/scanListContent.vue
index db60cc20..66311720 100644
--- a/webapp/src/components/tabContentComponents/scanListContent.vue
+++ b/webapp/src/components/tabContentComponents/scanListContent.vue
@@ -97,17 +97,13 @@
                 @error="modalError"
                 class="uk-button uk-width-1-2"
                 />
-                <action-button
-                thing="smart_scan"
-                action="download_zip"
-                submit-label="Download Stitch"
-                :can-terminate="false"
-                :submit-data="{ scan_name: item.name }"
-                :button-primary="true"
-                @response="downloadZipFile"
-                @error="modalError"
-                class="uk-button uk-width-1-2"
-                />
+                <a
+                  class="uk-button uk-button-primary uk-width-1-2"
+                  :class="item.stitch_available ? '' : 'disabled'"
+                  :href="downloadStitchFile( item.name )"
+                  download
+                  >Download Stitch</a
+                >
               <button
                 class="uk-button uk-button-default uk-width-1-1"
                 @click="deleteScan(item.name)"
@@ -231,6 +227,9 @@ export default {
   },
 
   methods: {
+    downloadStitchFile: function(name) {
+      return `${this.$store.getters.baseUri}/smart_scan/get_stitch/${name}`;
+    },
     thumbnailPath(scan_name) {
       return (
         `${this.$store.getters.baseUri}/smart_scan/scans/stitched_thumbnail.jpg?scan_name=` +
@@ -393,4 +392,9 @@ ul {
   text-align: center;
   font-weight: bold;
 }
+
+a.disabled {
+    pointer-events: none;
+    color: #ccc;
+}
 </style>
\ No newline at end of file

From 987807ec3b8461343d961923607989dbd3bf9d1e Mon Sep 17 00:00:00 2001
From: jaknapper <jaknapper@hotmail.com>
Date: Wed, 25 Jun 2025 18:12:12 +0100
Subject: [PATCH 03/12] Custom EndpointButton, Download logs using
 EndpointButton

---
 webapp/src/assets/less/theme.less             | 31 ++++--------
 .../labThingsComponents/endpointButton.vue    | 48 +++++++++++++++++++
 .../tabContentComponents/loggingContent.vue   | 16 ++++---
 .../tabContentComponents/scanListContent.vue  | 22 +++++----
 4 files changed, 79 insertions(+), 38 deletions(-)
 create mode 100644 webapp/src/components/labThingsComponents/endpointButton.vue

diff --git a/webapp/src/assets/less/theme.less b/webapp/src/assets/less/theme.less
index a8c6e80f..0b69d967 100644
--- a/webapp/src/assets/less/theme.less
+++ b/webapp/src/assets/less/theme.less
@@ -201,7 +201,6 @@ h4, .uk-h4 {
 
 .uk-card {
     border-radius: @paper-border-radius;
-    //border: 1px solid rgba(180, 180, 180, 0.25);
     box-shadow: @small-shadow;
 }
 
@@ -220,31 +219,13 @@ h4, .uk-h4 {
     margin: 0 auto;
 }
 
-.uk-card-default .uk-card-footer {
-    border-top: 1px solid rgba(180, 180, 180, 0.25);
-}
-
-.uk-card-primary .uk-card-footer {
-    border-top: 1px solid rgba(0, 0, 0, 0.075);
-}
-
-.uk-card-default {
-    color: @global-color;
-}
-
 .hook-inverse() {
 
     // Override background colour in dark mode
-    .uk-card-default {
+    .uk-card {
         background-color: #2a2a2a !important;
         color: @inverse-global-color;
     }
-
-    // Lighten on hover to show depth in dark mode
-    .uk-card-default:hover {
-        transition: background-color @animation-fast-duration ease;
-        background-color: #333 !important;
-    }
 }
 
 /*
@@ -385,7 +366,7 @@ a:hover {
 
 .hook-inverse() {
     .uk-button {
-        background-color: rgba(180, 180, 180, 0.15);
+        background-color: rgba(27, 13, 13, 0.15);
         color: @inverse-primary-muted-color;
         border-color: @inverse-primary-muted-color;
     }
@@ -396,7 +377,7 @@ a:hover {
     }
 
     .uk-button-primary {
-        background-color: rgba(180, 180, 180, 0.15);
+        background-color: rgb(0, 0, 0);
         color: @inverse-primary-muted-color;
         border-color: @inverse-primary-muted-color;
     }
@@ -408,6 +389,12 @@ a:hover {
     }
 }
 
+.disabled {
+  border: 1px solid #999999 !important;
+  background-color: #cccccc !important;
+  color: #919191 !important;
+}
+
 .uk-icon-button,
 .uk-icon-button:hover {
     text-decoration: none
diff --git a/webapp/src/components/labThingsComponents/endpointButton.vue b/webapp/src/components/labThingsComponents/endpointButton.vue
new file mode 100644
index 00000000..f626527a
--- /dev/null
+++ b/webapp/src/components/labThingsComponents/endpointButton.vue
@@ -0,0 +1,48 @@
+<template>
+    <a
+      class="uk-button"
+      :class="[isDisabled ? 'disabled' : '', buttonPrimary ? 'uk-button-primary' : 'uk-button-default']"
+      :href="URL"
+      download
+      > {{ buttonLabel }}</a
+    >
+</template>
+
+<script>
+
+export default {
+  name: "EndpointButton",
+
+  props: {
+    buttonPrimary: {
+      type: Boolean,
+      required: false,
+      default: true
+    },
+    URL: {
+      type: String,
+      required: true,
+    },
+    isDisabled: {
+      type: Boolean,
+      required: false,
+      default: false
+    },
+    destinationName: {
+      type: String,
+      required: false,
+      default: null
+    },
+    buttonLabel: {
+      type: String,
+      required: false,
+      default: "Download File"
+    }
+  },
+};
+</script>
+
+<style lang="less" scoped>
+@import "../../assets/less/theme.less";
+
+</style>
diff --git a/webapp/src/components/tabContentComponents/loggingContent.vue b/webapp/src/components/tabContentComponents/loggingContent.vue
index 38f3520c..f1628462 100644
--- a/webapp/src/components/tabContentComponents/loggingContent.vue
+++ b/webapp/src/components/tabContentComponents/loggingContent.vue
@@ -30,12 +30,12 @@
             </button>
           </div>
           <div>
-            <a
-              class="uk-button uk-button-default"
-              :href="logFileURI"
-              download="openflexure_microscope.log"
-              >Download Log File</a
-            >
+          <EndpointButton
+            class="uk-button uk-width-1-1"
+            :URL="logFileURI"
+            buttonLabel="Download Log File"
+            :buttonPrimary="false"
+            />
           </div>
         </div>
       </div>
@@ -94,12 +94,14 @@
 <script>
 import axios from "axios";
 import Paginate from "vuejs-paginate";
+import EndpointButton from "../labThingsComponents/endpointButton.vue";
 
 export default {
   name: "LoggingContent",
 
   components: {
-    Paginate
+    Paginate,
+    EndpointButton
   },
 
   data: function() {
diff --git a/webapp/src/components/tabContentComponents/scanListContent.vue b/webapp/src/components/tabContentComponents/scanListContent.vue
index 66311720..af6da18b 100644
--- a/webapp/src/components/tabContentComponents/scanListContent.vue
+++ b/webapp/src/components/tabContentComponents/scanListContent.vue
@@ -86,7 +86,9 @@
               </div>
               <h3 class="uk-card-title" style="text-align: center;">{{ item.name }}</h3>
               <div class="button-container">
+              <div class="uk-button-group" style="width:100%">
                 <action-button
+                class="uk-width-1-2"
                 thing="smart_scan"
                 action="download_zip"
                 submit-label="Download All"
@@ -95,15 +97,15 @@
                 :button-primary="true"
                 @response="downloadZipFile"
                 @error="modalError"
-                class="uk-button uk-width-1-2"
                 />
-                <a
-                  class="uk-button uk-button-primary uk-width-1-2"
-                  :class="item.stitch_available ? '' : 'disabled'"
-                  :href="downloadStitchFile( item.name )"
-                  download
-                  >Download Stitch</a
-                >
+                <EndpointButton
+                  class="uk-width-1-2"
+                  :buttonPrimary=true
+                  :isDisabled=!item.stitch_available
+                  :URL="downloadStitchFile( item.name )"
+                  buttonLabel="Download JPEG"
+                  />
+              </div>
               <button
                 class="uk-button uk-button-default uk-width-1-1"
                 @click="deleteScan(item.name)"
@@ -120,6 +122,7 @@
                 :button-primary="false"
                 :modal-progress="true"
                 @error="modalError"
+                @response="updateScans"
               />
               <button
                 v-if="item.dzi" class="uk-button uk-button-default uk-width-1-1"
@@ -151,11 +154,12 @@ import axios from "axios";
 import UIkit from "uikit";
 import actionButton from "../labThingsComponents/actionButton.vue";
 import OpenSeadragonViewer from "./scanListComponents/openSeadragonViewer.vue";
+import EndpointButton from "../labThingsComponents/endpointButton.vue";
 
 // Export main app
 export default {
   name: "ScanListContent",
-  components: { actionButton, OpenSeadragonViewer },
+  components: { actionButton, OpenSeadragonViewer, EndpointButton },
 
   data: function() {
     return {

From ceefc8322979c6ca26d530296f819b8b6540f304 Mon Sep 17 00:00:00 2001
From: jaknapper <jaknapper@hotmail.com>
Date: Wed, 25 Jun 2025 19:02:05 +0100
Subject: [PATCH 04/12] Better checking of whether we can stitch

---
 webapp/src/components/tabContentComponents/scanListContent.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/webapp/src/components/tabContentComponents/scanListContent.vue b/webapp/src/components/tabContentComponents/scanListContent.vue
index af6da18b..2fdbc801 100644
--- a/webapp/src/components/tabContentComponents/scanListContent.vue
+++ b/webapp/src/components/tabContentComponents/scanListContent.vue
@@ -116,7 +116,7 @@
                 submit-label="Stitch Images"
                 thing="smart_scan"
                 action="stitch_scan"
-                v-if="item.can_stitch | !item.dzi"
+                v-if="item.can_stitch | (item.stitch_available & !item.dzi)"
                 :can-terminate="false"
                 :submit-data="{ scan_name: item.name }"
                 :button-primary="false"

From daf2cee481b686534e147b6a9192a9182a94cf93 Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Mon, 30 Jun 2025 23:03:20 +0100
Subject: [PATCH 05/12] Add tests and correct stitch path

---
 .../scan_directories.py                       | 16 ++--
 tests/test_scan_directories.py                | 84 +++++++++++++++++--
 2 files changed, 87 insertions(+), 13 deletions(-)

diff --git a/src/openflexure_microscope_server/scan_directories.py b/src/openflexure_microscope_server/scan_directories.py
index 76fe0185..b5c3a73f 100644
--- a/src/openflexure_microscope_server/scan_directories.py
+++ b/src/openflexure_microscope_server/scan_directories.py
@@ -13,11 +13,12 @@ import zipfile
 
 from pydantic import BaseModel
 
-STITCH_SUFFIX = "_stitched.jpg"
 IMG_DIR_NAME = "images"
-IMAGE_REGEX = re.compile(r"-?[0-9]+_-?[0-9]+\.jpe?g$")
 SCAN_ZERO_PAD_DIGITS = 4
 
+STITCH_REGEX = re.compile(r"stitched\.jpe?g$")
+IMAGE_REGEX = re.compile(r"-?[0-9]+_-?[0-9]+\.jpe?g$")
+
 
 class NotEnoughFreeSpaceError(IOError):
     pass
@@ -98,11 +99,14 @@ class ScanDirectoryManager:
         return file_path
 
     def get_final_stitch(self, scan_name: str) -> Optional[str]:
-        """Return the file path for the final stitch.
+        """Return the file full path for the final stitch.
 
         If no final stitch is found, return None
         """
-        return ScanDirectory(scan_name, self.base_dir).get_final_stitch()
+        stitch_fname = ScanDirectory(scan_name, self.base_dir).get_final_stitch()
+        if stitch_fname is None:
+            return None
+        return self.get_file_from_img_dir(scan_name, stitch_fname)
 
     @property
     def all_scans(self) -> list[str]:
@@ -267,7 +271,7 @@ class ScanDirectory:
                 return scan_images
 
         if file_types in ["all", "stitches"]:
-            stitches = [i for i in folder_contents if i.endswith("_stitched.jpg")]
+            stitches = [i for i in folder_contents if STITCH_REGEX.search(i)]
             if file_types == "stitches":
                 return stitches
 
@@ -279,7 +283,7 @@ class ScanDirectory:
         return scan_images, stitches, dzi_files
 
     def get_final_stitch(self) -> Optional[str]:
-        """Return the file path for the final stitch.
+        """Return the filename for the final stitch (in the images dir)
 
         If no final stitch is found, return None
         """
diff --git a/tests/test_scan_directories.py b/tests/test_scan_directories.py
index ee76c9ab..0bde692c 100644
--- a/tests/test_scan_directories.py
+++ b/tests/test_scan_directories.py
@@ -32,10 +32,13 @@ def _clear_scan_dir() -> None:
 
 def _add_fake_image(scan_dir: ScanDirectory) -> None:
     """Make a fake image on disk in the scan directory"""
-    x_pos = random.randint(-100, 100)
-    y_pos = random.randint(-100, 100)
-    filename = f"image_{x_pos}_{y_pos}.jpg"
-    filepath = os.path.join(scan_dir.images_dir, filename)
+    unique = False
+    while not unique:
+        x_pos = random.randint(-10000, 10000)
+        y_pos = random.randint(-10000, 10000)
+        filename = f"image_{x_pos}_{y_pos}.jpg"
+        filepath = os.path.join(scan_dir.images_dir, filename)
+        unique = not os.path.exists(filepath)
     with open(filepath, "w") as f_obj:
         f_obj.write("fake")
 
@@ -211,13 +214,42 @@ def test_scan_info():
     assert not info.stitch_available
     assert info.dzi is None
 
-    # Add a fake scan and check this is recognised as a stitch not a scan image
+    # Add a fake stitched images and check this is recognised as a stitch not
+    # a scan image
     _add_fake_file(scan_dir, "fake_scan_0001_stitched.jpg", in_im_dir=True)
     info = scan_dir.scan_info()
     assert info.number_of_images == 17
     assert info.stitch_available
 
 
+def test_get_final_stitch():
+    """Check that the final stitch can be retrieved"""
+    _clear_scan_dir()
+    scan_dir_manager = ScanDirectoryManager(BASE_SCAN_DIR)
+    scan_dir = scan_dir_manager.new_scan_dir("fake_scan")
+
+    # Create some scan images files
+    for i in range(17):
+        _add_fake_image(scan_dir)
+
+    # No scans, so None should be returned, from both manager and scan dir
+    assert scan_dir_manager.get_final_stitch(scan_dir.name) is None
+    assert scan_dir.get_final_stitch() is None
+
+    fake_scan_name = "fake_scan_0001_stitched.jpg"
+    fake_scan_path = scan_dir_manager.get_file_from_img_dir(
+        scan_name=scan_dir.name,
+        filename="fake_scan_0001_stitched.jpg",
+        check_exists=False,
+    )
+    # Add a fake scan
+    _add_fake_file(scan_dir, fake_scan_name, in_im_dir=True)
+    # Manager returns full path
+    assert scan_dir_manager.get_final_stitch(scan_dir.name) == fake_scan_path
+    # ScanDirectory object returns just the filename
+    assert scan_dir.get_final_stitch() == fake_scan_name
+
+
 def test_empty_scan_info():
     """Test the scan info is correct even if the scan is empty"""
     _clear_scan_dir()
@@ -277,7 +309,7 @@ def test_creating_scan_dir_for_missing_scan():
     """Check creating ScanDirectory object for a dir that doesn't exist fails."""
     _clear_scan_dir()
     with pytest.raises(FileNotFoundError):
-        ScanDirectory(BASE_SCAN_DIR, "not_real_0001")
+        ScanDirectory("not_real_0001", BASE_SCAN_DIR)
 
 
 def test_none_returned_for_missing_images_dir():
@@ -290,12 +322,50 @@ def test_none_returned_for_missing_images_dir():
     """
     _clear_scan_dir()
     os.makedirs(os.path.join(BASE_SCAN_DIR, "fake_scan_0001"))
-    scan_dir = ScanDirectory(BASE_SCAN_DIR, "fake_scan_0001")
+    scan_dir = ScanDirectory("fake_scan_0001", BASE_SCAN_DIR)
     assert scan_dir.images_dir is None
     # Also check that get scan files returns and empty list
     assert scan_dir.get_scan_files() == []
 
 
+def test_find_files():
+    """Test the private _find_files method of ScanDirectories
+
+    Add files to directory and check expected returns.
+    """
+    _clear_scan_dir()
+    os.makedirs(os.path.join(BASE_SCAN_DIR, "fake_scan_0001", "images"))
+    scan_dir = ScanDirectory("fake_scan_0001", BASE_SCAN_DIR)
+
+    # For an empty directory, "all" is 3 empty lists
+    assert scan_dir._find_files("all") == ([], [], [])
+    # Other options are 1 empty list.
+    for file_type in ["scan_images", "stitches", "dzi"]:
+        assert scan_dir._find_files(file_type) == []
+
+    # Add a number of images
+    for i in range(2321):
+        _add_fake_image(scan_dir)
+
+    assert len(set(scan_dir._find_files("scan_images"))) == 2321
+    assert len(set(scan_dir._find_files("stitches"))) == 0
+    assert len(set(scan_dir._find_files("dzi"))) == 0
+
+    # Add and a stitched image
+    _add_fake_file(scan_dir, "fake_scan_0001_stitched.jpg", in_im_dir=True)
+
+    assert len(set(scan_dir._find_files("scan_images"))) == 2321
+    assert len(set(scan_dir._find_files("stitches"))) == 1
+    assert len(set(scan_dir._find_files("dzi"))) == 0
+
+    # Add and a dzi image
+    _add_fake_file(scan_dir, "fake_scan_0001.dzi", in_im_dir=True)
+
+    assert len(set(scan_dir._find_files("scan_images"))) == 2321
+    assert len(set(scan_dir._find_files("stitches"))) == 1
+    assert len(set(scan_dir._find_files("dzi"))) == 1
+
+
 DiskUsage = namedtuple("DiskUsage", ["total", "used", "free"])
 
 

From 3671d524993905c0c80c8f85568f7229ef3741ae Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Tue, 1 Jul 2025 09:04:14 +0100
Subject: [PATCH 06/12] Do not zip DZI files, or their associated tiles

---
 .../scan_directories.py                       | 27 +++++--
 tests/test_scan_directories.py                | 77 ++++++++++++++++++-
 2 files changed, 95 insertions(+), 9 deletions(-)

diff --git a/src/openflexure_microscope_server/scan_directories.py b/src/openflexure_microscope_server/scan_directories.py
index b5c3a73f..8f0e97d5 100644
--- a/src/openflexure_microscope_server/scan_directories.py
+++ b/src/openflexure_microscope_server/scan_directories.py
@@ -296,7 +296,7 @@ class ScanDirectory:
         """Return the modified time of the directory"""
         return max(os.stat(root).st_mtime for root, _, _ in os.walk(self.dir_path))
 
-    def scan_info(self):
+    def scan_info(self) -> ScanInfo:
         """Return the information for the scan directory as a ScanInfo object"""
 
         scan_images, stitches, dzi_files = self._find_files("all")
@@ -313,10 +313,20 @@ class ScanDirectory:
             dzi=dzi,
         )
 
-    def all_files(self):
-        """Return a list of all files in the scan dir relative to the dir"""
+    def all_files(self, skip_dirs: Optional[list[str]] = None) -> list[str]:
+        """Return a list of all files in the scan dir relative to the dir.
+
+        :param skip_dirs: Skip any file in a directory that is on this list. The list
+            should be the basename of the directory. e.g. "scan_0001_files" not
+            "images/scan_0001_files"
+        """
+        if skip_dirs is None:
+            skip_dirs = []
         files = []
-        for file_root, _, filenames in os.walk(self.dir_path):
+        for file_root, dirs, filenames in os.walk(self.dir_path, topdown=True):
+            # Skip any skipped directories.
+            # Note: we must use slice assignment to edit in place.
+            dirs[:] = [d for d in dirs if d not in skip_dirs]
             for filename in filenames:
                 full_path = os.path.join(file_root, filename)
                 files.append(os.path.relpath(full_path, self.dir_path))
@@ -338,10 +348,13 @@ class ScanDirectory:
         else:
             zip_files = []
 
+        # For each `filename.dzi` we need to skip the `filename_files` directory
+        dzi_dirs = [dzi[:-4] + "_files" for dzi in self._find_files("dzi")]
+
         with zipfile.ZipFile(zip_fname, mode="a") as scan_zip:
-            for file in self.all_files():
-                # Don't zip zipfiles, or files in the zip
-                if file.endswith(".zip") or file in zip_files:
+            for file in self.all_files(skip_dirs=dzi_dirs):
+                # Don't zip zipfiles, dzi files, or files already in the zip
+                if file.endswith((".zip", ".dzi")) or file in zip_files:
                     continue
                 # If this is not the final version, then only zip image files.
                 if not final_version and not IMAGE_REGEX.search(file):
diff --git a/tests/test_scan_directories.py b/tests/test_scan_directories.py
index 0bde692c..9cd3ae68 100644
--- a/tests/test_scan_directories.py
+++ b/tests/test_scan_directories.py
@@ -1,5 +1,6 @@
 import tempfile
 import os
+import math
 import shutil
 import logging
 import random
@@ -59,6 +60,40 @@ def _add_fake_file(
         f_obj.write("fake")
 
 
+def _make_fake_dzi(scan_dir: ScanDirectory, n_layers: int = 8) -> None:
+    """Create a fake DZI in a scan
+
+    :param n_layers: The number of layers of tiles. I.e. tile directories numbered
+        0...(n_layers-1) will be created. Default 8
+    """
+
+    # Add an a dzi image
+    dzi_fname = scan_dir.name + ".dzi"
+    dzi_path = os.path.join(scan_dir.images_dir, dzi_fname)
+    with open(dzi_path, "w") as f_obj:
+        f_obj.write("This should be xml")
+
+    # and the directory for the dzi tiles
+    dzi_tile_dir = scan_dir.name + "_files"
+    dzi_tile_dir_path = os.path.join(scan_dir.images_dir, dzi_tile_dir)
+    os.makedirs(dzi_tile_dir_path)
+
+    # this directory then contains a directories numbered from 0-n
+    for i in range(n_layers):
+        layer_dir_path = os.path.join(dzi_tile_dir_path, str(i))
+        os.makedirs(layer_dir_path)
+
+        # Number of images (in each axis) in this layer. Number of tiles doubles each
+        # layer, but the first few layers always have 1 image.
+        n_ims = math.ceil(2 ** (i - 4))
+        for x_index in range(n_ims):
+            for y_index in range(n_ims):
+                tile_name = f"{x_index}_{y_index}.jpg"
+                tile_path = os.path.join(layer_dir_path, tile_name)
+                with open(tile_path, "w") as f_obj:
+                    f_obj.write("This would normally be jpeg data")
+
+
 def test_basic_directory_operations():
     """Test some basic operations
 
@@ -284,6 +319,9 @@ def test_zipping_scan_data():
         _add_fake_file(scan_dir, "fake_scan_0001_stitched.jpg", in_im_dir=True)
         _add_fake_file(scan_dir, "zipfile.zip")
 
+        # This fake dzi should have loads of images. The DZI should not be zipped!
+        _make_fake_dzi(scan_dir)
+
         # zip the directory without setting as the final version. It should only
         # zip the 21 scan images
         if caller == "scan_dir":
@@ -305,6 +343,38 @@ def test_zipping_scan_data():
             assert not file.endswith(".zip")
 
 
+def test_all_files():
+    """Test all_files returns the path, and respects skipped directories"""
+    _clear_scan_dir()
+    scan_dir_manager = ScanDirectoryManager(BASE_SCAN_DIR)
+    scan_dir = scan_dir_manager.new_scan_dir("fake_scan")
+    # This fake dzi should have loads of images. The DZI should not be zipped!
+    _make_fake_dzi(scan_dir)
+    all_files = scan_dir.all_files()
+
+    # As standard for 8 layers there are 89 jpegs and 1 dzi file.
+    assert len(all_files) == 90
+    dzi_file = None
+    # Check all files exist
+    for file in all_files:
+        assert os.path.exists(os.path.join(scan_dir.dir_path, file))
+        if file.endswith(".dzi"):
+            # There is only 1 dzi file, so this should be None
+            assert dzi_file is None
+            dzi_file = file
+    # Once loop is complete there should be a dzi file
+    assert dzi_file is not None
+    # Get the dzi tile directory name
+    dzi_dir = os.path.basename(dzi_file[:-4] + "_files")
+
+    # Get all files skipping the dzi tile directory
+    all_files = scan_dir.all_files(skip_dirs=dzi_dir)
+    # There is now only one file
+    assert len(all_files) == 1
+    # It is the DZI file
+    assert all_files[0] == dzi_file
+
+
 def test_creating_scan_dir_for_missing_scan():
     """Check creating ScanDirectory object for a dir that doesn't exist fails."""
     _clear_scan_dir()
@@ -358,13 +428,16 @@ def test_find_files():
     assert len(set(scan_dir._find_files("stitches"))) == 1
     assert len(set(scan_dir._find_files("dzi"))) == 0
 
-    # Add and a dzi image
-    _add_fake_file(scan_dir, "fake_scan_0001.dzi", in_im_dir=True)
+    _make_fake_dzi(scan_dir)
 
     assert len(set(scan_dir._find_files("scan_images"))) == 2321
     assert len(set(scan_dir._find_files("stitches"))) == 1
     assert len(set(scan_dir._find_files("dzi"))) == 1
 
+    _, stitches, dzi_files = scan_dir._find_files("all")
+    assert stitches[0] == "fake_scan_0001_stitched.jpg"
+    assert dzi_files[0] == "fake_scan_0001.dzi"
+
 
 DiskUsage = namedtuple("DiskUsage", ["total", "used", "free"])
 

From 75eac81b801901039613bda96a371ab4c4a88dfd Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Tue, 1 Jul 2025 11:16:25 +0100
Subject: [PATCH 07/12] rename css disabled property to make it button
 specific, adjust darkmode disabled css

---
 webapp/src/assets/less/theme.less               | 17 ++++++++++++-----
 .../labThingsComponents/endpointButton.vue      |  2 +-
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/webapp/src/assets/less/theme.less b/webapp/src/assets/less/theme.less
index 0b69d967..c3c89bf6 100644
--- a/webapp/src/assets/less/theme.less
+++ b/webapp/src/assets/less/theme.less
@@ -17,6 +17,7 @@
 @global-primary-background: #C32280;
 
 @inverse-primary-muted-color: lighten(@global-primary-background, 15%);
+@darkened-primary-color: darken(@global-primary-background, 15%);
 @inverse-global-color: fade(@global-inverse-color, 80%);
 
 @global-border: #d5d5d5;
@@ -364,6 +365,12 @@ a:hover {
     border: 1px solid #f0506e;
 }
 
+.uk-button-disabled {
+    border: 1px solid #999999 !important;
+    background-color: #cccccc !important;
+    color: #919191 !important;
+}
+
 .hook-inverse() {
     .uk-button {
         background-color: rgba(27, 13, 13, 0.15);
@@ -387,12 +394,12 @@ a:hover {
         color: #fff;
         border-color: #fff;
     }
-}
 
-.disabled {
-  border: 1px solid #999999 !important;
-  background-color: #cccccc !important;
-  color: #919191 !important;
+    .uk-button-disabled {
+        border: 1px solid @darkened-primary-color !important;
+        background-color: #333333 !important;
+        color: #777777 !important;
+    }
 }
 
 .uk-icon-button,
diff --git a/webapp/src/components/labThingsComponents/endpointButton.vue b/webapp/src/components/labThingsComponents/endpointButton.vue
index f626527a..3083e100 100644
--- a/webapp/src/components/labThingsComponents/endpointButton.vue
+++ b/webapp/src/components/labThingsComponents/endpointButton.vue
@@ -1,7 +1,7 @@
 <template>
     <a
       class="uk-button"
-      :class="[isDisabled ? 'disabled' : '', buttonPrimary ? 'uk-button-primary' : 'uk-button-default']"
+      :class="[isDisabled ? 'uk-button-disabled' : '', buttonPrimary ? 'uk-button-primary' : 'uk-button-default']"
       :href="URL"
       download
       > {{ buttonLabel }}</a

From 9b78b4620d5421007d7e69df16b263ce7569a60d Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Tue, 1 Jul 2025 11:13:42 +0000
Subject: [PATCH 08/12] Fix disabled HTML button and apply code review
 suggestions for branch download-stitched-image

Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
---
 tests/test_scan_directories.py                                | 1 +
 webapp/src/components/labThingsComponents/endpointButton.vue  | 4 +++-
 .../src/components/tabContentComponents/scanListContent.vue   | 4 ----
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/tests/test_scan_directories.py b/tests/test_scan_directories.py
index 9cd3ae68..3f0a60c1 100644
--- a/tests/test_scan_directories.py
+++ b/tests/test_scan_directories.py
@@ -341,6 +341,7 @@ def test_zipping_scan_data():
         # Check the zips are not in the zip
         for file in zip_files:
             assert not file.endswith(".zip")
+            assert not file.endswith(".dzi")
 
 
 def test_all_files():
diff --git a/webapp/src/components/labThingsComponents/endpointButton.vue b/webapp/src/components/labThingsComponents/endpointButton.vue
index 3083e100..d7882ef6 100644
--- a/webapp/src/components/labThingsComponents/endpointButton.vue
+++ b/webapp/src/components/labThingsComponents/endpointButton.vue
@@ -44,5 +44,7 @@ export default {
 
 <style lang="less" scoped>
 @import "../../assets/less/theme.less";
-
+a.uk-button-disabled {
+  pointer-events: none;
+}
 </style>
diff --git a/webapp/src/components/tabContentComponents/scanListContent.vue b/webapp/src/components/tabContentComponents/scanListContent.vue
index 2fdbc801..5446a933 100644
--- a/webapp/src/components/tabContentComponents/scanListContent.vue
+++ b/webapp/src/components/tabContentComponents/scanListContent.vue
@@ -397,8 +397,4 @@ ul {
   font-weight: bold;
 }
 
-a.disabled {
-    pointer-events: none;
-    color: #ccc;
-}
 </style>
\ No newline at end of file

From 254305a7a55e8f42a31c37f50ace966cb99720b4 Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Tue, 1 Jul 2025 19:21:56 +0100
Subject: [PATCH 09/12] Clarify whether name or path is returned in scan
 directory functions

---
 .../scan_directories.py                       | 16 +++++++--------
 .../things/smart_scan.py                      |  8 ++++----
 tests/test_scan_directories.py                | 20 ++++++++++---------
 3 files changed, 23 insertions(+), 21 deletions(-)

diff --git a/src/openflexure_microscope_server/scan_directories.py b/src/openflexure_microscope_server/scan_directories.py
index 8f0e97d5..8adadfa0 100644
--- a/src/openflexure_microscope_server/scan_directories.py
+++ b/src/openflexure_microscope_server/scan_directories.py
@@ -70,10 +70,10 @@ class ScanDirectoryManager:
         """
         return os.path.join(self._base_scan_dir, scan_name, IMG_DIR_NAME)
 
-    def get_file_from(
+    def get_file_path_from(
         self, scan_name: str, filename: str, check_exists: bool = False
     ) -> Optional[str]:
-        """Return the file path for the file within a scan directory
+        """Return the file full path for the file within a scan directory
 
         If check_exists is True then None will be returned if the file does
         not exist.
@@ -84,10 +84,10 @@ class ScanDirectoryManager:
                 return None
         return file_path
 
-    def get_file_from_img_dir(
+    def get_file_path_from_img_dir(
         self, scan_name: str, filename: str, check_exists: bool = False
     ) -> Optional[str]:
-        """Return the file path for the file within a scan directory
+        """Return the full file path for the file within a scan directory
 
         If check_exists is True, None is returned if the file does not exist. If False
         then the path is returned anyway
@@ -98,15 +98,15 @@ class ScanDirectoryManager:
                 return None
         return file_path
 
-    def get_final_stitch(self, scan_name: str) -> Optional[str]:
+    def get_final_stitch_path(self, scan_name: str) -> Optional[str]:
         """Return the file full path for the final stitch.
 
         If no final stitch is found, return None
         """
-        stitch_fname = ScanDirectory(scan_name, self.base_dir).get_final_stitch()
+        stitch_fname = ScanDirectory(scan_name, self.base_dir).get_final_stitch_name()
         if stitch_fname is None:
             return None
-        return self.get_file_from_img_dir(scan_name, stitch_fname)
+        return self.get_file_path_from_img_dir(scan_name, stitch_fname)
 
     @property
     def all_scans(self) -> list[str]:
@@ -282,7 +282,7 @@ class ScanDirectory:
 
         return scan_images, stitches, dzi_files
 
-    def get_final_stitch(self) -> Optional[str]:
+    def get_final_stitch_name(self) -> Optional[str]:
         """Return the filename for the final stitch (in the images dir)
 
         If no final stitch is found, return None
diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py
index 36e73273..22937721 100644
--- a/src/openflexure_microscope_server/things/smart_scan.py
+++ b/src/openflexure_microscope_server/things/smart_scan.py
@@ -580,7 +580,7 @@ class SmartScanThing(Thing):
 
         This endpoint allows files to be downloaded from a scan.
         """
-        preview_path = self._scan_dir_manager.get_file_from_img_dir(
+        preview_path = self._scan_dir_manager.get_file_path_from_img_dir(
             scan_name=scan_name, filename="stitched_thumbnail.jpg", check_exists=True
         )
         if preview_path is None:
@@ -684,7 +684,7 @@ class SmartScanThing(Thing):
         Will only return a file ending in suffix STITCH_SUFFIX
         Note: when downloading this, the default filename will be `scan_name`.jpeg"""
 
-        stitch_path = self._scan_dir_manager.get_final_stitch(scan_name)
+        stitch_path = self._scan_dir_manager.get_final_stitch_path(scan_name)
 
         if stitch_path is None:
             raise HTTPException(404, "File not found")
@@ -758,7 +758,7 @@ class SmartScanThing(Thing):
         if not self.latest_scan_name:
             return None
 
-        return self._scan_dir_manager.get_file_from_img_dir(
+        return self._scan_dir_manager.get_file_path_from_img_dir(
             scan_name=self.latest_scan_name, filename="preview.jpg", check_exists=True
         )
 
@@ -899,7 +899,7 @@ class SmartScanThing(Thing):
         Note that as this is a thing_action it needs the logger passed as
         a variable if called from another thing action
         """
-        json_fpath = self._scan_dir_manager.get_file_from_img_dir(
+        json_fpath = self._scan_dir_manager.get_file_path_from_img_dir(
             scan_name=scan_name, filename=SCAN_DATA_FILENAME
         )
 
diff --git a/tests/test_scan_directories.py b/tests/test_scan_directories.py
index 3f0a60c1..22f88957 100644
--- a/tests/test_scan_directories.py
+++ b/tests/test_scan_directories.py
@@ -122,17 +122,19 @@ def test_basic_directory_operations():
     assert scan_dir_manager.img_dir_for(scan_name) == scan_im_dir
 
     # Get the path of a fake file
-    fake_file = scan_dir_manager.get_file_from(scan_name, "foo.zip")
+    fake_file = scan_dir_manager.get_file_path_from(scan_name, "foo.zip")
     assert fake_file == os.path.join(scan_path, "foo.zip")
     # But this is none if we check it exists
-    fake_file = scan_dir_manager.get_file_from(scan_name, "foo.zip", check_exists=True)
+    fake_file = scan_dir_manager.get_file_path_from(
+        scan_name, "foo.zip", check_exists=True
+    )
     assert fake_file is None
 
     # Get the path of another fake file
-    fake_file = scan_dir_manager.get_file_from_img_dir(scan_name, "bar.img")
+    fake_file = scan_dir_manager.get_file_path_from_img_dir(scan_name, "bar.img")
     assert fake_file == os.path.join(scan_im_dir, "bar.img")
     # But this is none if we check it exists
-    fake_file = scan_dir_manager.get_file_from_img_dir(
+    fake_file = scan_dir_manager.get_file_path_from_img_dir(
         scan_name, "bar.img", check_exists=True
     )
     assert fake_file is None
@@ -268,11 +270,11 @@ def test_get_final_stitch():
         _add_fake_image(scan_dir)
 
     # No scans, so None should be returned, from both manager and scan dir
-    assert scan_dir_manager.get_final_stitch(scan_dir.name) is None
-    assert scan_dir.get_final_stitch() is None
+    assert scan_dir_manager.get_final_stitch_path(scan_dir.name) is None
+    assert scan_dir.get_final_stitch_name() is None
 
     fake_scan_name = "fake_scan_0001_stitched.jpg"
-    fake_scan_path = scan_dir_manager.get_file_from_img_dir(
+    fake_scan_path = scan_dir_manager.get_file_path_from_img_dir(
         scan_name=scan_dir.name,
         filename="fake_scan_0001_stitched.jpg",
         check_exists=False,
@@ -280,9 +282,9 @@ def test_get_final_stitch():
     # Add a fake scan
     _add_fake_file(scan_dir, fake_scan_name, in_im_dir=True)
     # Manager returns full path
-    assert scan_dir_manager.get_final_stitch(scan_dir.name) == fake_scan_path
+    assert scan_dir_manager.get_final_stitch_path(scan_dir.name) == fake_scan_path
     # ScanDirectory object returns just the filename
-    assert scan_dir.get_final_stitch() == fake_scan_name
+    assert scan_dir.get_final_stitch_name() == fake_scan_name
 
 
 def test_empty_scan_info():

From 7295b86cf66e1602fa9b7eeaa86008cade4be2a7 Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Tue, 1 Jul 2025 19:42:09 +0100
Subject: [PATCH 10/12] Split up ScanDirectory._find_files into seperate
 functions

---
 .../scan_directories.py                       | 56 ++++++++++---------
 tests/test_scan_directories.py                | 39 +++++++------
 2 files changed, 53 insertions(+), 42 deletions(-)

diff --git a/src/openflexure_microscope_server/scan_directories.py b/src/openflexure_microscope_server/scan_directories.py
index 8adadfa0..7aac9fc6 100644
--- a/src/openflexure_microscope_server/scan_directories.py
+++ b/src/openflexure_microscope_server/scan_directories.py
@@ -5,7 +5,7 @@ Currently it handles scan getting information from a information from a scan dir
 eventually is should handle all the file system operation for smart_scan.
 """
 
-from typing import Optional, Literal
+from typing import Optional
 import os
 import re
 import shutil
@@ -254,40 +254,40 @@ class ScanDirectory:
             return []
         return os.listdir(self.images_dir)
 
-    def _find_files(
-        self, file_types=Literal["all", "scan_images", "stitches", "dzi"]
-    ) -> tuple[list[str], list[str], list[str]] | list[str]:
-        folder_contents = self.get_scan_files()
+    def _extract_scan_images(self, file_list: list[str]):
+        """Extract files which match the naming convention for scan images
 
-        # Return empty lists if no folder contents.
-        if not folder_contents:
-            if file_types == "all":
-                return [], [], []
-            return []
+        :param file_list: The list of files to search. Normally this would be
+        `self.get_scan_files()`
 
-        if file_types in ["all", "scan_images"]:
-            scan_images = [i for i in folder_contents if IMAGE_REGEX.search(i)]
-            if file_types == "scan_images":
-                return scan_images
+        :returns: The list of files that match the naming convention for scan images
+        """
+        return [i for i in file_list if IMAGE_REGEX.search(i)]
 
-        if file_types in ["all", "stitches"]:
-            stitches = [i for i in folder_contents if STITCH_REGEX.search(i)]
-            if file_types == "stitches":
-                return stitches
+    def _extract_final_stitches(self, file_list: list[str]):
+        """Extract files which match the naming convention for final stitches
 
-        if file_types in ["all", "dzi"]:
-            dzi_files = [i for i in folder_contents if i.endswith("dzi")]
-            if file_types == "dzi":
-                return dzi_files
+        :param file_list: The list of files to search.
 
-        return scan_images, stitches, dzi_files
+        :returns: The list of files that match the naming convention for final stitches
+        """
+        return [i for i in file_list if STITCH_REGEX.search(i)]
+
+    def _extract_dzi_files(self, file_list: list[str]):
+        """Extract files which match the naming convention for dzi_files
+
+        :param file_list: The list of files to search.
+
+        :returns: The list of files that match the naming convention for dzi_files
+        """
+        return [i for i in file_list if i.endswith("dzi")]
 
     def get_final_stitch_name(self) -> Optional[str]:
         """Return the filename for the final stitch (in the images dir)
 
         If no final stitch is found, return None
         """
-        stitches = self._find_files("stitches")
+        stitches = self._extract_final_stitches(self.get_scan_files())
         if not stitches:
             return None
         return stitches[0]
@@ -299,7 +299,10 @@ class ScanDirectory:
     def scan_info(self) -> ScanInfo:
         """Return the information for the scan directory as a ScanInfo object"""
 
-        scan_images, stitches, dzi_files = self._find_files("all")
+        scan_files = self.get_scan_files()
+        scan_images = self._extract_scan_images(scan_files)
+        stitches = self._extract_final_stitches(scan_files)
+        dzi_files = self._extract_dzi_files(scan_files)
         number_of_images = len(scan_images)
         stitch_available = len(stitches) > 0
         dzi = None if not dzi_files else str(dzi_files[0])
@@ -349,7 +352,8 @@ class ScanDirectory:
             zip_files = []
 
         # For each `filename.dzi` we need to skip the `filename_files` directory
-        dzi_dirs = [dzi[:-4] + "_files" for dzi in self._find_files("dzi")]
+        dzi_files = self._extract_dzi_files(self.get_scan_files())
+        dzi_dirs = [dzi[:-4] + "_files" for dzi in dzi_files]
 
         with zipfile.ZipFile(zip_fname, mode="a") as scan_zip:
             for file in self.all_files(skip_dirs=dzi_dirs):
diff --git a/tests/test_scan_directories.py b/tests/test_scan_directories.py
index 22f88957..3fb59760 100644
--- a/tests/test_scan_directories.py
+++ b/tests/test_scan_directories.py
@@ -401,7 +401,7 @@ def test_none_returned_for_missing_images_dir():
     assert scan_dir.get_scan_files() == []
 
 
-def test_find_files():
+def test_extracting_files():
     """Test the private _find_files method of ScanDirectories
 
     Add files to directory and check expected returns.
@@ -410,34 +410,41 @@ def test_find_files():
     os.makedirs(os.path.join(BASE_SCAN_DIR, "fake_scan_0001", "images"))
     scan_dir = ScanDirectory("fake_scan_0001", BASE_SCAN_DIR)
 
-    # For an empty directory, "all" is 3 empty lists
-    assert scan_dir._find_files("all") == ([], [], [])
-    # Other options are 1 empty list.
-    for file_type in ["scan_images", "stitches", "dzi"]:
-        assert scan_dir._find_files(file_type) == []
+    # Starting all lists should be empty
+    scan_files = scan_dir.get_scan_files()
+    assert scan_dir._extract_scan_images(scan_files) == []
+    assert scan_dir._extract_final_stitches(scan_files) == []
+    assert scan_dir._extract_dzi_files(scan_files) == []
 
     # Add a number of images
     for i in range(2321):
         _add_fake_image(scan_dir)
 
-    assert len(set(scan_dir._find_files("scan_images"))) == 2321
-    assert len(set(scan_dir._find_files("stitches"))) == 0
-    assert len(set(scan_dir._find_files("dzi"))) == 0
+    scan_files = scan_dir.get_scan_files()
+    assert len(set(scan_dir._extract_scan_images(scan_files))) == 2321
+    assert len(set(scan_dir._extract_final_stitches(scan_files))) == 0
+    assert len(set(scan_dir._extract_dzi_files(scan_files))) == 0
 
     # Add and a stitched image
     _add_fake_file(scan_dir, "fake_scan_0001_stitched.jpg", in_im_dir=True)
 
-    assert len(set(scan_dir._find_files("scan_images"))) == 2321
-    assert len(set(scan_dir._find_files("stitches"))) == 1
-    assert len(set(scan_dir._find_files("dzi"))) == 0
+    scan_files = scan_dir.get_scan_files()
+    assert len(set(scan_dir._extract_scan_images(scan_files))) == 2321
+    assert len(set(scan_dir._extract_final_stitches(scan_files))) == 1
+    assert len(set(scan_dir._extract_dzi_files(scan_files))) == 0
 
     _make_fake_dzi(scan_dir)
 
-    assert len(set(scan_dir._find_files("scan_images"))) == 2321
-    assert len(set(scan_dir._find_files("stitches"))) == 1
-    assert len(set(scan_dir._find_files("dzi"))) == 1
+    # check totals are still correct after adding a dzi with lots of tiles.
+    scan_files = scan_dir.get_scan_files()
+    scan_images = scan_dir._extract_scan_images(scan_files)
+    stitches = scan_dir._extract_final_stitches(scan_files)
+    dzi_files = scan_dir._extract_dzi_files(scan_files)
+    assert len(set(scan_images)) == 2321
+    assert len(set(stitches)) == 1
+    assert len(set(dzi_files)) == 1
 
-    _, stitches, dzi_files = scan_dir._find_files("all")
+    # And check the names are as expected
     assert stitches[0] == "fake_scan_0001_stitched.jpg"
     assert dzi_files[0] == "fake_scan_0001.dzi"
 

From 2e18c2017a6012d2f557e57f724174b286a16774 Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Wed, 2 Jul 2025 09:39:33 +0000
Subject: [PATCH 11/12] Apply suggestions from code review of branch
 download-stitched-image

Co-authored-by: Beth Probert <beth_probert@outlook.com>
---
 src/openflexure_microscope_server/scan_directories.py | 2 +-
 tests/test_scan_directories.py                        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/openflexure_microscope_server/scan_directories.py b/src/openflexure_microscope_server/scan_directories.py
index 7aac9fc6..361abf40 100644
--- a/src/openflexure_microscope_server/scan_directories.py
+++ b/src/openflexure_microscope_server/scan_directories.py
@@ -73,7 +73,7 @@ class ScanDirectoryManager:
     def get_file_path_from(
         self, scan_name: str, filename: str, check_exists: bool = False
     ) -> Optional[str]:
-        """Return the file full path for the file within a scan directory
+        """Return the full file path for the file within a scan directory
 
         If check_exists is True then None will be returned if the file does
         not exist.
diff --git a/tests/test_scan_directories.py b/tests/test_scan_directories.py
index 3fb59760..d1a61f0b 100644
--- a/tests/test_scan_directories.py
+++ b/tests/test_scan_directories.py
@@ -356,7 +356,7 @@ def test_all_files():
     all_files = scan_dir.all_files()
 
     # As standard for 8 layers there are 89 jpegs and 1 dzi file.
-    assert len(all_files) == 90
+    assert len(set(all_files)) == 90
     dzi_file = None
     # Check all files exist
     for file in all_files:

From f3a873ae5857daf7636cdb83bc8951616223c251 Mon Sep 17 00:00:00 2001
From: Beth Probert <beth_probert@outlook.com>
Date: Wed, 2 Jul 2025 09:51:27 +0000
Subject: [PATCH 12/12] Apply suggestions from code review of branch
 download-stitched-image

Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
---
 tests/test_scan_directories.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_scan_directories.py b/tests/test_scan_directories.py
index d1a61f0b..6df56f1b 100644
--- a/tests/test_scan_directories.py
+++ b/tests/test_scan_directories.py
@@ -357,6 +357,7 @@ def test_all_files():
 
     # As standard for 8 layers there are 89 jpegs and 1 dzi file.
     assert len(set(all_files)) == 90
+    assert len(all_files) == 90
     dzi_file = None
     # Check all files exist
     for file in all_files: