From 5b5fd1d07d2b92209486125d1ff436a03dfa570a Mon Sep 17 00:00:00 2001
From: Jun Aishima <jaishima@bnl.gov>
Date: Wed, 1 Apr 2026 13:18:49 -0400
Subject: [PATCH 01/12] initial commit for vlm snapshot exporter

---
 prefect_vlm_snapshot_exporter.py | 185 +++++++++++++++++++++++++++++++
 1 file changed, 185 insertions(+)
 create mode 100644 prefect_vlm_snapshot_exporter.py

diff --git a/prefect_vlm_snapshot_exporter.py b/prefect_vlm_snapshot_exporter.py
new file mode 100644
index 0000000..a9ddfa2
--- /dev/null
+++ b/prefect_vlm_snapshot_exporter.py
@@ -0,0 +1,185 @@
+# from prefect import flow, task, get_run_logger
+# from prefect.blocks.system import Secret
+# from tiled.client import from_profile
+
+import time as ttime
+import numpy as np
+import os
+from skimage import io
+from PIL import Image, ImageDraw, ImageFont
+import matplotlib.pyplot as plt
+
+
+# api_key = Secret.load("tiled-srx-api-key", _sync=True).get()
+# tiled_client = from_profile("nsls2", api_key=api_key)["srx"]
+# tiled_client_raw = tiled_client["raw"]
+
+
+# @flow(log_prints=True)
+# def vlm_image_exporter(ref):
+#     logger = get_run_logger()
+#     logger.info('')
+
+#     scan_id = tiled_client_raw[uid].start['scan_id']
+#     logger.info(f'Looking for snapshots in scan {scan_id}.')
+
+#     export_vlm_image(scan_id,
+#                      overlay=True,
+#                      raw_image=True,
+#                      image_type='.tif')
+#     logger.info(f'Finished exporting any snapshots in scan {scan_id}.')
+
+
+# @task
+def export_vlm_image(scan_id,
+                     wd=None,
+                     overlay=True,
+                     raw_image=True,
+                     image_type='.tif',
+                     autoscale=True
+                     ):
+    # logger = get_run_logger()
+
+    # Pseudocode
+    # overlays == True
+    #       raw_images == True:
+    #           Saves both raw images and overlays
+    #       raw_images == False:
+    #           Saves only overlaid images
+    # overlays == False
+    #       raw_images == True:
+    #           Saves only raw images
+    #       raw_images == False:
+    #           raises RuntimeError
+
+    # Initial checks
+    # Does scan exist
+    scan_id = int(scan_id)    
+    h = tiled_client_raw[scan_id]
+
+    # VLM image data acquired?
+    if 'camera_snapshot' not in h:
+        warn_str = f'No VLM images found for scan {scan_id}.'
+        # logger.info(warn_str)
+        return    
+    
+    # Logical combinations
+    if not overlay and not raw_image:
+        err_str = "One or both of 'overlay' and 'raw_image' must be True."
+        raise ValueError(err_str)
+
+    image_type = str(image_type)
+    if image_type[0] != '.':
+        image_type = '.' + image_type
+    supported_image_types = {'.tif', '.tiff', '.png', '.bmp', '.jpeg'}
+    if image_type not in supported_image_types:
+        err_str = (f"Image type of ({image_type}) is not supported. "
+                   + f"Only supported image types are {supported_image_types}.")
+        raise TypeError(err_str)
+    
+    if wd is None:
+        proposal_id = h.start['proposal']['proposal_id']
+        cycle = h.start['cycle']
+        wd = f'/nsls2/data3/srx/proposals/{cycle}/pass-{proposal_id}/'
+    
+    # Create sub-folder
+    wd = f'{wd}vlm_snapshots/'
+    os.makedirs(wd, exist_ok=True)
+    
+    images = h['camera_snapshot']['data']['nano_vlm_image'][:, 0].astype(np.uint16)
+
+    # logger.info('VLM images found; writing images to folder.')
+    for image, title in zip(images, ['before', 'after']):
+        # Normalize
+        image = image.astype(np.float64)
+        if autoscale:
+            image -= image.mean() - 2 * image.std()
+            image /= image.mean() + 2 * image.std()
+            image[image < 0] = 0
+            image[image > 1] = 1
+        else:
+            image -= image.min()
+            image /= image.max()
+
+        # Return raw tiff
+        if raw_image:
+            io.imsave(os.path.join(wd, f'scan{scan_id}_VLM_image_{title}{image_type}'),
+                      (image * 65535).astype(np.uint16),
+                      check_contrast=False)
+        if overlay:
+            marker = tuple([h.start['scan']['detectors']['nano_vlm'][f'cross_position_{a}'] for a in ['x', 'y']])
+
+            overlayed_image = _overlay_image(image.copy(), marker)
+            io.imsave(os.path.join(wd, f'scan{scan_id}_VLM_image_{title}_overlay{image_type}'),
+                      overlayed_image.astype(np.uint8),
+                      check_contrast=False)
+
+
+def _overlay_image(image, marker):
+
+    # Hard-coded scale
+    scale = 0.5 # pixels/um
+    bar_length_um = 200
+    bar_length_px = int(bar_length_um / scale)
+    bar_height_px = 15
+    unit_name = 'μm'
+
+    position = 'lower_right'
+    color = (255, 0, 0)
+
+    # Convert to grayscale and leave contiguous in memory
+    image = plt.cm.gray(image / image.max())[:, :, :3].copy()
+    image = (image * 255).astype(np.uint8)
+    image = Image.fromarray(image)
+    draw = ImageDraw.Draw(image)
+
+    # Get image dimensions
+    w, h = image.size
+
+    # Define padding
+    v_padding = 75
+    h_padding = 50
+
+    # Determine position
+    bar_x1 = w - h_padding - bar_length_px
+    bar_y1 = h - v_padding - bar_height_px
+    text_x = bar_x1 + bar_length_px // 2
+    text_y = bar_y1 + bar_height_px + 5
+
+    bar_x2 = bar_x1 + bar_length_px
+    bar_y2 = bar_y1 + bar_height_px
+
+    # Draw the scale bar rectangle
+    # print(f'{bar_x1=}', f'{bar_x2=}')
+    # print(f'{bar_y1=}', f'{bar_y2=}')
+
+    # Add scalebar
+    draw.rectangle([bar_x1, bar_y1, bar_x2, bar_y2], fill=color)
+
+    # Add text label
+    text = f"{bar_length_um} {unit_name}"
+    font = ImageFont.truetype("DejaVuSans.ttf", 50)
+    text_width, text_height = draw.textbbox((0, 0), text, font=font)[2:]
+    # print(f'{text_width=}', f'{text_height=}')
+    draw.text((text_x - (text_width // 2),
+               text_y), text, font=font, fill=color,
+               stroke_width=1, # 2 for bold
+              )
+
+    # Add beam position indicator (+)
+    marker_size = 50
+    marker_width = 10
+    draw.line((marker[0] - marker_size // 2,
+               marker[1],
+               marker[0] + marker_size // 2,
+               marker[1]),
+               fill=color,
+               width=marker_width)
+    draw.line((marker[0],
+               marker[1] - marker_size // 2,
+               marker[0],
+               marker[1] + marker_size // 2),
+               fill=color,
+               width=marker_width)           
+
+    return np.asarray(image, dtype=np.uint8)

From 51f3bdeec8606e440fa41688cb0d14df5f31739f Mon Sep 17 00:00:00 2001
From: Jun Aishima <jaishima@bnl.gov>
Date: Wed, 1 Apr 2026 13:26:56 -0400
Subject: [PATCH 02/12] remove unused code, get_run() from data_validation

---
 prefect_vlm_snapshot_exporter.py | 44 ++++++++++++++------------------
 1 file changed, 19 insertions(+), 25 deletions(-)

diff --git a/prefect_vlm_snapshot_exporter.py b/prefect_vlm_snapshot_exporter.py
index a9ddfa2..146d3b7 100644
--- a/prefect_vlm_snapshot_exporter.py
+++ b/prefect_vlm_snapshot_exporter.py
@@ -1,44 +1,38 @@
-# from prefect import flow, task, get_run_logger
-# from prefect.blocks.system import Secret
-# from tiled.client import from_profile
-
+from prefect import flow, task, get_run_logger
 import time as ttime
 import numpy as np
 import os
 from skimage import io
 from PIL import Image, ImageDraw, ImageFont
 import matplotlib.pyplot as plt
+from data_validation import get_run
 
 
-# api_key = Secret.load("tiled-srx-api-key", _sync=True).get()
-# tiled_client = from_profile("nsls2", api_key=api_key)["srx"]
-# tiled_client_raw = tiled_client["raw"]
-
-
-# @flow(log_prints=True)
-# def vlm_image_exporter(ref):
-#     logger = get_run_logger()
-#     logger.info('')
+@flow(log_prints=True)
+def vlm_image_exporter(ref, api_key=None):
+    logger = get_run_logger()
+    logger.info('')
 
-#     scan_id = tiled_client_raw[uid].start['scan_id']
-#     logger.info(f'Looking for snapshots in scan {scan_id}.')
+    scan_id = get_run(uid, api_key=api_key).start['scan_id']
+    logger.info(f'Looking for snapshots in scan {scan_id}.')
 
-#     export_vlm_image(scan_id,
-#                      overlay=True,
-#                      raw_image=True,
-#                      image_type='.tif')
-#     logger.info(f'Finished exporting any snapshots in scan {scan_id}.')
+    export_vlm_image(scan_id,
+                     overlay=True,
+                     raw_image=True,
+                     image_type='.tif')
+    logger.info(f'Finished exporting any snapshots in scan {scan_id}.')
 
 
-# @task
+@task
 def export_vlm_image(scan_id,
                      wd=None,
                      overlay=True,
                      raw_image=True,
                      image_type='.tif',
-                     autoscale=True
+                     autoscale=True,
+                     api_key=None
                      ):
-    # logger = get_run_logger()
+    logger = get_run_logger()
 
     # Pseudocode
     # overlays == True
@@ -55,12 +49,12 @@ def export_vlm_image(scan_id,
     # Initial checks
     # Does scan exist
     scan_id = int(scan_id)    
-    h = tiled_client_raw[scan_id]
+    h = get_run(scan_id, api_key=api_key)
 
     # VLM image data acquired?
     if 'camera_snapshot' not in h:
         warn_str = f'No VLM images found for scan {scan_id}.'
-        # logger.info(warn_str)
+        logger.info(warn_str)
         return    
     
     # Logical combinations

From 14172ed8c8b739b6cbd638ec565997851bd3f1fe Mon Sep 17 00:00:00 2001
From: Jun Aishima <jaishima@bnl.gov>
Date: Wed, 1 Apr 2026 13:28:05 -0400
Subject: [PATCH 03/12] use /nsls2/data instead of changeable /nsls2/data3

---
 prefect_vlm_snapshot_exporter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/prefect_vlm_snapshot_exporter.py b/prefect_vlm_snapshot_exporter.py
index 146d3b7..73401a6 100644
--- a/prefect_vlm_snapshot_exporter.py
+++ b/prefect_vlm_snapshot_exporter.py
@@ -74,7 +74,7 @@ def export_vlm_image(scan_id,
     if wd is None:
         proposal_id = h.start['proposal']['proposal_id']
         cycle = h.start['cycle']
-        wd = f'/nsls2/data3/srx/proposals/{cycle}/pass-{proposal_id}/'
+        wd = f'/nsls2/data/srx/proposals/{cycle}/pass-{proposal_id}/'
     
     # Create sub-folder
     wd = f'{wd}vlm_snapshots/'

From 154c23c6dc667b13edeb1b13e17bc66587c473ef Mon Sep 17 00:00:00 2001
From: Jun Aishima <jaishima@bnl.gov>
Date: Wed, 1 Apr 2026 13:33:26 -0400
Subject: [PATCH 04/12] shorten new exporter filename

---
 prefect_vlm_snapshot_exporter.py => vlm_snapshot_exporter.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename prefect_vlm_snapshot_exporter.py => vlm_snapshot_exporter.py (100%)

diff --git a/prefect_vlm_snapshot_exporter.py b/vlm_snapshot_exporter.py
similarity index 100%
rename from prefect_vlm_snapshot_exporter.py
rename to vlm_snapshot_exporter.py

From a8e0e50b0fdcdd75bd853eaa9d0ad462c378282d Mon Sep 17 00:00:00 2001
From: Jun Aishima <jaishima@bnl.gov>
Date: Wed, 1 Apr 2026 13:35:02 -0400
Subject: [PATCH 05/12] update to add pillow

---
 pixi.lock | 2724 +++++++++++++++++++++++++++--------------------------
 pixi.toml |    1 +
 2 files changed, 1392 insertions(+), 1333 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index 5a802ec..f17639a 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -30,37 +30,37 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.3.0-pyh71513ae_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/awkward-2.8.6-pyhe01879c_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/awkward-cpp-48-py312h1e80e48_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.9.0-h0fbd49f_19.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.2-he7b75e1_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.4-hb03c661_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.3.1-h92c474e_6.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.5.5-h149bd38_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.10.4-h37a7233_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.21.2-h6252d9a_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-mqtt-0.13.3-h19deb91_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.8.6-h800fcd2_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.2.4-h92c474e_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.2.7-h92c474e_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.33.1-hb4fd278_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-sdk-cpp-1.11.606-h31ade35_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-core-cpp-1.16.0-h3a458e0_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-identity-cpp-1.12.0-ha729027_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-blobs-cpp-12.14.0-hb1c9500_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-common-cpp-12.10.0-hebae86a_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-files-datalake-cpp-12.12.0-h8b27e44_3.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.9.3-hef928c7_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.13-h2c9d079_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.6-hb03c661_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.3.1-h8b1a151_9.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.5.7-h28f887f_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.10.7-ha8fc4e3_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.23.3-hdaf4b65_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-mqtt-0.13.3-hc63082f_11.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.11.3-h06ab39a_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.2.4-h8b1a151_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.2.7-h8b1a151_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.35.4-h8824e59_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-sdk-cpp-1.11.606-h20b40b1_10.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-core-cpp-1.16.1-h3a458e0_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-identity-cpp-1.13.2-h3a5f585_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-blobs-cpp-12.16.0-h75daedc_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-common-cpp-12.12.0-h3d7a050_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-files-datalake-cpp-12.14.0-hd454692_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/bcrypt-5.0.0-py312h868fb18_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/blinker-1.9.0-pyhff2d567_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.6-he440d0b_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/bluesky-tiled-plugins-2.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/bokeh-3.7.3-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/boltons-25.0.0-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hb03c661_4.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hb03c661_4.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py312h1289d80_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.2.0-hed03a55_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.2.0-hb03c661_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py312hdb49522_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/brunsli-0.1-h9c3ff4c_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-2.21.3-h4cfbee9_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-2.22.0-hc31b594_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cached-property-1.5.2-hd8ed1ab_1.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2
@@ -108,14 +108,14 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.1-ha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.3-ha770c72_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/fsspec-2025.7.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/future-1.0.0-pyhd8ed1ab_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.42.12-h7b179bb_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.44.4-h2b0a6b4_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gflags-2.2.2-h5888daf_1005.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/glib-tools-2.84.3-hf516916_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/glib-tools-2.86.0-hf516916_0.conda
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+  - c-blosc2 >=2.22.0,<2.23.0a0
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   - brunsli >=0.1,<1.0a0
   - bzip2 >=1.0.8,<2.0a0
-  - c-blosc2 >=2.21.2,<2.22.0a0
+  - c-blosc2 >=2.22.0,<2.23.0a0
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   - giflib >=5.2.2,<5.3.0a0
   - jxrlib >=1.1,<1.2.0a0
-  - lcms2 >=2.17,<3.0a0
+  - lcms2 >=2.18,<3.0a0
   - lerc >=4.0.0,<5.0a0
   - libaec >=1.1.4,<2.0a0
   - libavif16 >=1.3.0,<2.0a0
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-  - libbrotlienc >=1.1.0,<1.2.0a0
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+  - libbrotlidec >=1.2.0,<1.3.0a0
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   - libcxx >=19
-  - libdeflate >=1.24,<1.25.0a0
-  - libjpeg-turbo >=3.1.0,<4.0a0
+  - libdeflate >=1.25,<1.26.0a0
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   - libjxl >=0.11,<0.12.0a0
   - liblzma >=5.8.1,<6.0a0
-  - libpng >=1.6.50,<1.7.0a0
-  - libtiff >=4.7.0,<4.8.0a0
+  - libpng >=1.6.54,<1.7.0a0
+  - libtiff >=4.7.1,<4.8.0a0
   - libwebp-base >=1.6.0,<2.0a0
   - libzlib >=1.3.1,<2.0a0
   - libzopfli >=1.0.3,<1.1.0a0
   - lz4-c >=1.10.0,<1.11.0a0
   - numpy >=1.23,<3
-  - openjpeg >=2.5.3,<3.0a0
+  - openjpeg >=2.5.4,<3.0a0
+  - openjph >=0.26.0,<0.27.0a0
   - python >=3.12,<3.13.0a0
   - python >=3.12,<3.13.0a0 *_cpython
   - python_abi 3.12.* *_cp312
   - snappy >=1.2.2,<1.3.0a0
   - zfp >=1.0.1,<2.0a0
-  - zlib-ng >=2.2.5,<2.3.0a0
+  - zlib-ng >=2.3.2,<2.4.0a0
   - zstd >=1.5.7,<1.6.0a0
   license: BSD-3-Clause
   license_family: BSD
   purls:
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-  size: 1660602
-  timestamp: 1757611208796
+  size: 1554488
+  timestamp: 1768379327542
 - conda: https://conda.anaconda.org/conda-forge/noarch/imageio-2.37.0-pyhfb79c49_0.conda
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   timestamp: 1733636905835
-- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.17-h717163a_0.conda
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-  md5: 000e85703f0fd9594c81710dd5066471
+- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.18-h0c24ade_0.conda
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+  md5: 6f2e2c8f58160147c4d1c6f4c14cbac4
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-  - libgcc >=13
-  - libjpeg-turbo >=3.0.0,<4.0a0
-  - libtiff >=4.7.0,<4.8.0a0
+  - libgcc >=14
+  - libjpeg-turbo >=3.1.2,<4.0a0
+  - libtiff >=4.7.1,<4.8.0a0
   license: MIT
   license_family: MIT
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/lcms2-2.17-h72f5680_0.conda
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   license_family: MIT
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-  md5: 92a61fd30b19ebd5c1621a5bfe6d8b5f
+  size: 226870
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+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/lcms2-2.18-hdfa7624_0.conda
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+  md5: 6631a7bd2335bb9699b1dbc234b19784
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-  - libtiff >=4.7.0,<4.8.0a0
+  - libjpeg-turbo >=3.1.2,<4.0a0
+  - libtiff >=4.7.1,<4.8.0a0
   license: MIT
   license_family: MIT
   purls: []
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-  timestamp: 1739161108467
+  size: 211756
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda
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-  md5: c100b9a4d6c72c691543af69f707df51
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libarrow-21.0.0-h2c50142_16_cpu.conda
+  build_number: 16
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+  md5: 086cf583b140f3412dad39a74fd3934f
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-  - aws-crt-cpp >=0.33.1,<0.33.2.0a0
+  - aws-crt-cpp >=0.35.4,<0.35.5.0a0
   - aws-sdk-cpp >=1.11.606,<1.11.607.0a0
-  - azure-core-cpp >=1.16.0,<1.16.1.0a0
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-  - azure-storage-files-datalake-cpp >=12.12.0,<12.12.1.0a0
+  - azure-core-cpp >=1.16.1,<1.16.2.0a0
+  - azure-identity-cpp >=1.13.2,<1.13.3.0a0
+  - azure-storage-blobs-cpp >=12.16.0,<12.16.1.0a0
+  - azure-storage-files-datalake-cpp >=12.14.0,<12.14.1.0a0
   - bzip2 >=1.0.8,<2.0a0
   - glog >=0.7.1,<0.8.0a0
   - libabseil * cxx17*
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-  - libbrotlidec >=1.1.0,<1.2.0a0
-  - libbrotlienc >=1.1.0,<1.2.0a0
+  - libbrotlidec >=1.2.0,<1.3.0a0
+  - libbrotlienc >=1.2.0,<1.3.0a0
   - libgcc >=14
   - libgoogle-cloud >=2.39.0,<2.40.0a0
   - libgoogle-cloud-storage >=2.39.0,<2.40.0a0
@@ -5568,7 +5576,7 @@ packages:
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   - lz4-c >=1.10.0,<1.11.0a0
-  - orc >=2.2.0,<2.2.1.0a0
+  - orc >=2.2.2,<2.2.3.0a0
   - snappy >=1.2.2,<1.3.0a0
   - zstd >=1.5.7,<1.6.0a0
   constrains:
@@ -5578,26 +5586,26 @@ packages:
   license: Apache-2.0
   license_family: APACHE
   purls: []
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-  timestamp: 1754309354037
-- conda: https://conda.anaconda.org/conda-forge/osx-64/libarrow-21.0.0-h3202d62_8_cpu.conda
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-  md5: c0a631268e4ee440e3a83a5928de30f9
+  size: 6194071
+  timestamp: 1769167631964
+- conda: https://conda.anaconda.org/conda-forge/osx-64/libarrow-21.0.0-h57e2ed6_16_cpu.conda
+  build_number: 16
+  sha256: bc7f085aecb71db2bf734ba56582d17210c9b36f9ee50cebd160f0cac47c0e84
+  md5: 1424991d2c88ad3f92f85e4f6b5811b7
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-  - aws-crt-cpp >=0.34.4,<0.34.5.0a0
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   - aws-sdk-cpp >=1.11.606,<1.11.607.0a0
-  - azure-core-cpp >=1.16.0,<1.16.1.0a0
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-  - azure-storage-files-datalake-cpp >=12.12.0,<12.12.1.0a0
+  - azure-core-cpp >=1.16.1,<1.16.2.0a0
+  - azure-identity-cpp >=1.13.2,<1.13.3.0a0
+  - azure-storage-blobs-cpp >=12.16.0,<12.16.1.0a0
+  - azure-storage-files-datalake-cpp >=12.14.0,<12.14.1.0a0
   - bzip2 >=1.0.8,<2.0a0
   - glog >=0.7.1,<0.8.0a0
   - libabseil * cxx17*
   - libabseil >=20250512.1,<20250513.0a0
-  - libbrotlidec >=1.1.0,<1.2.0a0
-  - libbrotlienc >=1.1.0,<1.2.0a0
+  - libbrotlidec >=1.2.0,<1.3.0a0
+  - libbrotlienc >=1.2.0,<1.3.0a0
   - libcxx >=19
   - libgoogle-cloud >=2.39.0,<2.40.0a0
   - libgoogle-cloud-storage >=2.39.0,<2.40.0a0
@@ -5605,36 +5613,36 @@ packages:
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   - libzlib >=1.3.1,<2.0a0
   - lz4-c >=1.10.0,<1.11.0a0
-  - orc >=2.2.1,<2.2.2.0a0
+  - orc >=2.2.2,<2.2.3.0a0
   - snappy >=1.2.2,<1.3.0a0
   - zstd >=1.5.7,<1.6.0a0
   constrains:
+  - parquet-cpp <0.0a0
   - apache-arrow-proc =*=cpu
   - arrow-cpp <0.0a0
-  - parquet-cpp <0.0a0
   license: Apache-2.0
   license_family: APACHE
   purls: []
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-  timestamp: 1759483300750
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libarrow-21.0.0-hd43feaf_8_cpu.conda
-  build_number: 8
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-  md5: 92d5cc7e1d494aeb82db5b2faa33b28c
+  size: 4193851
+  timestamp: 1769166030460
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libarrow-21.0.0-hdf148b7_16_cpu.conda
+  build_number: 16
+  sha256: ddc5e07243adf8320dcd093f7fb7449cd5b9248529d9ed48d47392d8ad3ff937
+  md5: dbaaf00c50a1242206ef85a61cce4082
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   - aws-sdk-cpp >=1.11.606,<1.11.607.0a0
-  - azure-core-cpp >=1.16.0,<1.16.1.0a0
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-  - azure-storage-files-datalake-cpp >=12.12.0,<12.12.1.0a0
+  - azure-core-cpp >=1.16.1,<1.16.2.0a0
+  - azure-identity-cpp >=1.13.2,<1.13.3.0a0
+  - azure-storage-blobs-cpp >=12.16.0,<12.16.1.0a0
+  - azure-storage-files-datalake-cpp >=12.14.0,<12.14.1.0a0
   - bzip2 >=1.0.8,<2.0a0
   - glog >=0.7.1,<0.8.0a0
   - libabseil * cxx17*
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-  - libbrotlidec >=1.1.0,<1.2.0a0
-  - libbrotlienc >=1.1.0,<1.2.0a0
+  - libbrotlidec >=1.2.0,<1.3.0a0
+  - libbrotlienc >=1.2.0,<1.3.0a0
   - libcxx >=19
   - libgoogle-cloud >=2.39.0,<2.40.0a0
   - libgoogle-cloud-storage >=2.39.0,<2.40.0a0
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   - lz4-c >=1.10.0,<1.11.0a0
-  - orc >=2.2.1,<2.2.2.0a0
+  - orc >=2.2.2,<2.2.3.0a0
   - snappy >=1.2.2,<1.3.0a0
   - zstd >=1.5.7,<1.6.0a0
   constrains:
-  - parquet-cpp <0.0a0
   - arrow-cpp <0.0a0
+  - parquet-cpp <0.0a0
   - apache-arrow-proc =*=cpu
   license: Apache-2.0
   license_family: APACHE
   purls: []
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-  timestamp: 1759481958097
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+  - libarrow 21.0.0 h2c50142_16_cpu
+  - libarrow-compute 21.0.0 h8c2c5c3_16_cpu
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   license: Apache-2.0
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   purls: []
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   timestamp: 1756829016061
-- conda: https://conda.anaconda.org/conda-forge/linux-64/s2n-1.5.23-h8e187f5_0.conda
-  sha256: 016fe83763bc837beb205732411583179e2aac1cdef40225d4ad5eeb1bc7b837
-  md5: edd15d7a5914dc1d87617a2b7c582d23
+- conda: https://conda.anaconda.org/conda-forge/linux-64/s2n-1.6.2-he8a4886_1.conda
+  sha256: dec76e9faa3173579d34d226dbc91892417a80784911daf8e3f0eb9bad19d7a6
+  md5: bade189a194e66b93c03021bd36c337b
   depends:
   - __glibc >=2.17,<3.0.a0
   - libgcc >=14
-  - openssl >=3.5.1,<4.0a0
+  - openssl >=3.5.4,<4.0a0
   license: Apache-2.0
   license_family: Apache
   purls: []
-  size: 383097
-  timestamp: 1753407970803
+  size: 394197
+  timestamp: 1765160261434
 - conda: https://conda.anaconda.org/conda-forge/linux-64/scikit-beam-0.0.27-py312h4f23490_1.conda
   sha256: fd3856e924d40a043d8c7716b415dc926200e4db303243985cfd31b9a87e8072
   md5: c312f4294592f2780551332f4458dcba
@@ -13106,43 +13165,42 @@ packages:
   - pkg:pypi/zipp?source=hash-mapping
   size: 22963
   timestamp: 1749421737203
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-hb9d3cd8_2.conda
-  sha256: 5d7c0e5f0005f74112a34a7425179f4eb6e73c92f5d109e6af4ddeca407c92ab
-  md5: c9f075ab2f33b3bbee9e62d4ad0a6cd8
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.2-h25fd6f3_2.conda
+  sha256: 245c9ee8d688e23661b95e3c6dd7272ca936fabc03d423cdb3cdee1bbcf9f2f2
+  md5: c2a01a08fc991620a74b32420e97868a
   depends:
   - __glibc >=2.17,<3.0.a0
-  - libgcc >=13
-  - libzlib 1.3.1 hb9d3cd8_2
+  - libzlib 1.3.2 h25fd6f3_2
   license: Zlib
   license_family: Other
   purls: []
-  size: 92286
-  timestamp: 1727963153079
-- conda: https://conda.anaconda.org/conda-forge/osx-64/zlib-1.3.1-hd23fc13_2.conda
-  sha256: 219edbdfe7f073564375819732cbf7cc0d7c7c18d3f546a09c2dfaf26e4d69f3
-  md5: c989e0295dcbdc08106fe5d9e935f0b9
+  size: 95931
+  timestamp: 1774072620848
+- conda: https://conda.anaconda.org/conda-forge/osx-64/zlib-1.3.2-hbb4bfdb_2.conda
+  sha256: 5dd728cebca2e96fa48d41661f1a35ed0ee3cb722669eee4e2d854c6745655eb
+  md5: 6276aa61ffc361cbf130d78cfb88a237
   depends:
-  - __osx >=10.13
-  - libzlib 1.3.1 hd23fc13_2
+  - __osx >=11.0
+  - libzlib 1.3.2 hbb4bfdb_2
   license: Zlib
   license_family: Other
   purls: []
-  size: 88544
-  timestamp: 1727963189976
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-1.3.1-h8359307_2.conda
-  sha256: 58f8860756680a4831c1bf4f294e2354d187f2e999791d53b1941834c4b37430
-  md5: e3170d898ca6cb48f1bb567afb92f775
+  size: 92411
+  timestamp: 1774073075482
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-1.3.2-h8088a28_2.conda
+  sha256: 8dd2ac25f0ba714263aac5832d46985648f4bfb9b305b5021d702079badc08d2
+  md5: f1c0bce276210bed45a04949cfe8dc20
   depends:
   - __osx >=11.0
-  - libzlib 1.3.1 h8359307_2
+  - libzlib 1.3.2 h8088a28_2
   license: Zlib
   license_family: Other
   purls: []
-  size: 77606
-  timestamp: 1727963209370
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.2.5-hde8ca8f_0.conda
-  sha256: 3a8e7798deafd0722b6b5da50c36b7f361a80b30165d600f7760d569a162ff95
-  md5: 1920c3502e7f6688d650ab81cd3775fd
+  size: 81123
+  timestamp: 1774072974535
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.3.3-hceb46e0_1.conda
+  sha256: ea4e50c465d70236408cb0bfe0115609fd14db1adcd8bd30d8918e0291f8a75f
+  md5: 2aadb0d17215603a82a2a6b0afd9a4cb
   depends:
   - __glibc >=2.17,<3.0.a0
   - libgcc >=14
@@ -13150,30 +13208,30 @@ packages:
   license: Zlib
   license_family: Other
   purls: []
-  size: 110843
-  timestamp: 1754587144298
-- conda: https://conda.anaconda.org/conda-forge/osx-64/zlib-ng-2.2.5-he7f0fdc_0.conda
-  sha256: ed46538570cf655326a4e80f72a7c03185adc493b53ec58371d3ec6d0fa7b5d3
-  md5: acdf87296c0cd71e61a740dbcd5b6ff5
+  size: 122618
+  timestamp: 1770167931827
+- conda: https://conda.anaconda.org/conda-forge/osx-64/zlib-ng-2.3.3-h8bce59a_1.conda
+  sha256: 4a1beb656761c7d8c9a53474bfd3932c30d82af5d93a32b8ef626c01c059d981
+  md5: b3ecb6480fd46194e3f7dd0ff4445dff
   depends:
   - __osx >=10.13
   - libcxx >=19
   license: Zlib
   license_family: Other
   purls: []
-  size: 109109
-  timestamp: 1754587436654
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-ng-2.2.5-hf787086_0.conda
-  sha256: 4b4220f03844aaaffa7868023963415e14cddd456f00b8fa78ee4a16fecd1b60
-  md5: fb78d469f8e0f1eb5bbbfd249aeed447
+  size: 120464
+  timestamp: 1770168263684
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-ng-2.3.3-hed4e4f5_1.conda
+  sha256: a339606a6b224bb230ff3d711e801934f3b3844271df9720165e0353716580d4
+  md5: d99c2a23a31b0172e90f456f580b695e
   depends:
   - __osx >=11.0
   - libcxx >=19
   license: Zlib
   license_family: Other
   purls: []
-  size: 87638
-  timestamp: 1754587529491
+  size: 94375
+  timestamp: 1770168363685
 - conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.25.0-py312h5253ce2_0.conda
   sha256: 1a3beda8068b55639edb92da8e0dc2d487e2a11aba627f709aab1d3cd5dd271c
   md5: 05d73100768745631ab3de9dc1e08da2
diff --git a/pixi.toml b/pixi.toml
index bc75d5c..40178af 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -12,6 +12,7 @@ xraylib = "*"
 scikit-beam = "*"
 pre-commit = ">=4.3.0,<5"
 databroker = "*"
+pillow = ">=12.2.0,<13"
 
 [pypi-dependencies]
 pyxrf = { git = "https://github.com/NSLS2/pyxrf.git", rev="7b7d868" }

From 367fd0a48c35d08c967b5bd2b5c848807f2afa07 Mon Sep 17 00:00:00 2001
From: Jun Aishima <jaishima@bnl.gov>
Date: Wed, 1 Apr 2026 13:50:00 -0400
Subject: [PATCH 06/12] add exporter to vlm snapshot exporter, remove overlays,
 write image with PIL

---
 end_of_run_workflow.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/end_of_run_workflow.py b/end_of_run_workflow.py
index 4ac4b3d..136c70f 100644
--- a/end_of_run_workflow.py
+++ b/end_of_run_workflow.py
@@ -6,6 +6,7 @@
 
 from xanes_exporter import xanes_exporter
 from xrf_hdf5_exporter import xrf_hdf5_exporter
+from vlm_snapshot_exporter import vlm_image_exporter
 from logscan import logscan
 from dotenv import load_dotenv
 import os

From 2544a1c869aa840352b7fc226124bba7d4596013 Mon Sep 17 00:00:00 2001
From: Jun Aishima <jaishima@bnl.gov>
Date: Wed, 1 Apr 2026 13:55:57 -0400
Subject: [PATCH 07/12] add vlm exporter, add dry_run and api_key, streamline
 image_type

---
 end_of_run_workflow.py   |   1 +
 vlm_snapshot_exporter.py | 129 ++++++---------------------------------
 2 files changed, 19 insertions(+), 111 deletions(-)

diff --git a/end_of_run_workflow.py b/end_of_run_workflow.py
index 136c70f..22494fc 100644
--- a/end_of_run_workflow.py
+++ b/end_of_run_workflow.py
@@ -90,5 +90,6 @@ def end_of_run_workflow(stop_doc, api_key=None, dry_run=False):
     # data_validation(uid, return_state=True, api_key=api)
     xanes_exporter(uid, api_key=api_key, dry_run=dry_run)
     xrf_hdf5_exporter(uid, api_key=api_key, dry_run=dry_run)
+    vlm_image_exporter(uid, api_key=api_key)
     logscan(uid, api_key=api_key, dry_run=dry_run)
     log_completion()
diff --git a/vlm_snapshot_exporter.py b/vlm_snapshot_exporter.py
index 73401a6..a61dea4 100644
--- a/vlm_snapshot_exporter.py
+++ b/vlm_snapshot_exporter.py
@@ -9,7 +9,7 @@
 
 
 @flow(log_prints=True)
-def vlm_image_exporter(ref, api_key=None):
+def vlm_image_exporter(ref, api_key=None, dry_run=False):
     logger = get_run_logger()
     logger.info('')
 
@@ -19,7 +19,8 @@ def vlm_image_exporter(ref, api_key=None):
     export_vlm_image(scan_id,
                      overlay=True,
                      raw_image=True,
-                     image_type='.tif')
+                     api_key=api_key,
+                     dry_run=dry_run)
     logger.info(f'Finished exporting any snapshots in scan {scan_id}.')
 
 
@@ -28,9 +29,9 @@ def export_vlm_image(scan_id,
                      wd=None,
                      overlay=True,
                      raw_image=True,
-                     image_type='.tif',
                      autoscale=True,
-                     api_key=None
+                     api_key=None,
+                     dry_run=False,
                      ):
     logger = get_run_logger()
 
@@ -55,21 +56,7 @@ def export_vlm_image(scan_id,
     if 'camera_snapshot' not in h:
         warn_str = f'No VLM images found for scan {scan_id}.'
         logger.info(warn_str)
-        return    
-    
-    # Logical combinations
-    if not overlay and not raw_image:
-        err_str = "One or both of 'overlay' and 'raw_image' must be True."
-        raise ValueError(err_str)
-
-    image_type = str(image_type)
-    if image_type[0] != '.':
-        image_type = '.' + image_type
-    supported_image_types = {'.tif', '.tiff', '.png', '.bmp', '.jpeg'}
-    if image_type not in supported_image_types:
-        err_str = (f"Image type of ({image_type}) is not supported. "
-                   + f"Only supported image types are {supported_image_types}.")
-        raise TypeError(err_str)
+        return
     
     if wd is None:
         proposal_id = h.start['proposal']['proposal_id']
@@ -80,100 +67,20 @@ def export_vlm_image(scan_id,
     wd = f'{wd}vlm_snapshots/'
     os.makedirs(wd, exist_ok=True)
     
-    images = h['camera_snapshot']['data']['nano_vlm_image'][:, 0].astype(np.uint16)
+    images = h['camera_snapshot']['data']['nano_vlm_image'][:, 0].astype(np.float64)
 
     # logger.info('VLM images found; writing images to folder.')
     for image, title in zip(images, ['before', 'after']):
         # Normalize
-        image = image.astype(np.float64)
-        if autoscale:
-            image -= image.mean() - 2 * image.std()
-            image /= image.mean() + 2 * image.std()
-            image[image < 0] = 0
-            image[image > 1] = 1
+        image -= image.mean() - 2 * image.std()
+        image /= image.mean() + 2 * image.std()
+        image[image < 0] = 0
+        image[image > 1] = 1
+
+        # Return raw png
+        image = Image.fromArray((image * 65535).astype(np.uint16))
+        filename = os.path.join(wd, f'scan{scan_id}_VLM_image_{title}.png')
+        if dry_run:
+            logger.info(f"Dry run: Not saving image to {filename}")
         else:
-            image -= image.min()
-            image /= image.max()
-
-        # Return raw tiff
-        if raw_image:
-            io.imsave(os.path.join(wd, f'scan{scan_id}_VLM_image_{title}{image_type}'),
-                      (image * 65535).astype(np.uint16),
-                      check_contrast=False)
-        if overlay:
-            marker = tuple([h.start['scan']['detectors']['nano_vlm'][f'cross_position_{a}'] for a in ['x', 'y']])
-
-            overlayed_image = _overlay_image(image.copy(), marker)
-            io.imsave(os.path.join(wd, f'scan{scan_id}_VLM_image_{title}_overlay{image_type}'),
-                      overlayed_image.astype(np.uint8),
-                      check_contrast=False)
-
-
-def _overlay_image(image, marker):
-
-    # Hard-coded scale
-    scale = 0.5 # pixels/um
-    bar_length_um = 200
-    bar_length_px = int(bar_length_um / scale)
-    bar_height_px = 15
-    unit_name = 'μm'
-
-    position = 'lower_right'
-    color = (255, 0, 0)
-
-    # Convert to grayscale and leave contiguous in memory
-    image = plt.cm.gray(image / image.max())[:, :, :3].copy()
-    image = (image * 255).astype(np.uint8)
-    image = Image.fromarray(image)
-    draw = ImageDraw.Draw(image)
-
-    # Get image dimensions
-    w, h = image.size
-
-    # Define padding
-    v_padding = 75
-    h_padding = 50
-
-    # Determine position
-    bar_x1 = w - h_padding - bar_length_px
-    bar_y1 = h - v_padding - bar_height_px
-    text_x = bar_x1 + bar_length_px // 2
-    text_y = bar_y1 + bar_height_px + 5
-
-    bar_x2 = bar_x1 + bar_length_px
-    bar_y2 = bar_y1 + bar_height_px
-
-    # Draw the scale bar rectangle
-    # print(f'{bar_x1=}', f'{bar_x2=}')
-    # print(f'{bar_y1=}', f'{bar_y2=}')
-
-    # Add scalebar
-    draw.rectangle([bar_x1, bar_y1, bar_x2, bar_y2], fill=color)
-
-    # Add text label
-    text = f"{bar_length_um} {unit_name}"
-    font = ImageFont.truetype("DejaVuSans.ttf", 50)
-    text_width, text_height = draw.textbbox((0, 0), text, font=font)[2:]
-    # print(f'{text_width=}', f'{text_height=}')
-    draw.text((text_x - (text_width // 2),
-               text_y), text, font=font, fill=color,
-               stroke_width=1, # 2 for bold
-              )
-
-    # Add beam position indicator (+)
-    marker_size = 50
-    marker_width = 10
-    draw.line((marker[0] - marker_size // 2,
-               marker[1],
-               marker[0] + marker_size // 2,
-               marker[1]),
-               fill=color,
-               width=marker_width)
-    draw.line((marker[0],
-               marker[1] - marker_size // 2,
-               marker[0],
-               marker[1] + marker_size // 2),
-               fill=color,
-               width=marker_width)           
-
-    return np.asarray(image, dtype=np.uint8)
+            image.save(filename)

From 2788fcc59ff86cda8c6fbbe73d75241c6f5a0b22 Mon Sep 17 00:00:00 2001
From: Jun Aishima <jaishima@bnl.gov>
Date: Wed, 1 Apr 2026 14:22:05 -0400
Subject: [PATCH 08/12] pre-commit lint fixes

---
 vlm_snapshot_exporter.py | 64 +++++++++++++++++++---------------------
 1 file changed, 30 insertions(+), 34 deletions(-)

diff --git a/vlm_snapshot_exporter.py b/vlm_snapshot_exporter.py
index a61dea4..d7e7ff6 100644
--- a/vlm_snapshot_exporter.py
+++ b/vlm_snapshot_exporter.py
@@ -1,38 +1,34 @@
 from prefect import flow, task, get_run_logger
-import time as ttime
 import numpy as np
 import os
-from skimage import io
-from PIL import Image, ImageDraw, ImageFont
-import matplotlib.pyplot as plt
+from PIL import Image
 from data_validation import get_run
 
 
 @flow(log_prints=True)
 def vlm_image_exporter(ref, api_key=None, dry_run=False):
     logger = get_run_logger()
-    logger.info('')
+    logger.info("")
 
-    scan_id = get_run(uid, api_key=api_key).start['scan_id']
-    logger.info(f'Looking for snapshots in scan {scan_id}.')
+    scan_id = get_run(uid, api_key=api_key).start["scan_id"]
+    logger.info(f"Looking for snapshots in scan {scan_id}.")
 
-    export_vlm_image(scan_id,
-                     overlay=True,
-                     raw_image=True,
-                     api_key=api_key,
-                     dry_run=dry_run)
-    logger.info(f'Finished exporting any snapshots in scan {scan_id}.')
+    export_vlm_image(
+        scan_id, overlay=True, raw_image=True, api_key=api_key, dry_run=dry_run
+    )
+    logger.info(f"Finished exporting any snapshots in scan {scan_id}.")
 
 
 @task
-def export_vlm_image(scan_id,
-                     wd=None,
-                     overlay=True,
-                     raw_image=True,
-                     autoscale=True,
-                     api_key=None,
-                     dry_run=False,
-                     ):
+def export_vlm_image(
+    scan_id,
+    wd=None,
+    overlay=True,
+    raw_image=True,
+    autoscale=True,
+    api_key=None,
+    dry_run=False,
+):
     logger = get_run_logger()
 
     # Pseudocode
@@ -49,28 +45,28 @@ def export_vlm_image(scan_id,
 
     # Initial checks
     # Does scan exist
-    scan_id = int(scan_id)    
+    scan_id = int(scan_id)
     h = get_run(scan_id, api_key=api_key)
 
     # VLM image data acquired?
-    if 'camera_snapshot' not in h:
-        warn_str = f'No VLM images found for scan {scan_id}.'
+    if "camera_snapshot" not in h:
+        warn_str = f"No VLM images found for scan {scan_id}."
         logger.info(warn_str)
         return
-    
+
     if wd is None:
-        proposal_id = h.start['proposal']['proposal_id']
-        cycle = h.start['cycle']
-        wd = f'/nsls2/data/srx/proposals/{cycle}/pass-{proposal_id}/'
-    
+        proposal_id = h.start["proposal"]["proposal_id"]
+        cycle = h.start["cycle"]
+        wd = f"/nsls2/data/srx/proposals/{cycle}/pass-{proposal_id}/"
+
     # Create sub-folder
-    wd = f'{wd}vlm_snapshots/'
+    wd = f"{wd}vlm_snapshots/"
     os.makedirs(wd, exist_ok=True)
-    
-    images = h['camera_snapshot']['data']['nano_vlm_image'][:, 0].astype(np.float64)
+
+    images = h["camera_snapshot"]["data"]["nano_vlm_image"][:, 0].astype(np.float64)
 
     # logger.info('VLM images found; writing images to folder.')
-    for image, title in zip(images, ['before', 'after']):
+    for image, title in zip(images, ["before", "after"]):
         # Normalize
         image -= image.mean() - 2 * image.std()
         image /= image.mean() + 2 * image.std()
@@ -79,7 +75,7 @@ def export_vlm_image(scan_id,
 
         # Return raw png
         image = Image.fromArray((image * 65535).astype(np.uint16))
-        filename = os.path.join(wd, f'scan{scan_id}_VLM_image_{title}.png')
+        filename = os.path.join(wd, f"scan{scan_id}_VLM_image_{title}.png")
         if dry_run:
             logger.info(f"Dry run: Not saving image to {filename}")
         else:

From f22dca180e836e818584d037443edd16e19343ef Mon Sep 17 00:00:00 2001
From: Jun Aishima <jaishima@bnl.gov>
Date: Wed, 1 Apr 2026 14:25:11 -0400
Subject: [PATCH 09/12] fix bad variable name - pre-commit lint

---
 vlm_snapshot_exporter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vlm_snapshot_exporter.py b/vlm_snapshot_exporter.py
index d7e7ff6..886da11 100644
--- a/vlm_snapshot_exporter.py
+++ b/vlm_snapshot_exporter.py
@@ -10,7 +10,7 @@ def vlm_image_exporter(ref, api_key=None, dry_run=False):
     logger = get_run_logger()
     logger.info("")
 
-    scan_id = get_run(uid, api_key=api_key).start["scan_id"]
+    scan_id = get_run(ref, api_key=api_key).start["scan_id"]
     logger.info(f"Looking for snapshots in scan {scan_id}.")
 
     export_vlm_image(

From 959ce84033f283296d2458e4eb180e2e4a0c8ec2 Mon Sep 17 00:00:00 2001
From: Jun Aishima <jaishima@bnl.gov>
Date: Thu, 2 Apr 2026 13:18:41 -0400
Subject: [PATCH 10/12] fix spelling of function

---
 vlm_snapshot_exporter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vlm_snapshot_exporter.py b/vlm_snapshot_exporter.py
index 886da11..7b56378 100644
--- a/vlm_snapshot_exporter.py
+++ b/vlm_snapshot_exporter.py
@@ -74,7 +74,7 @@ def export_vlm_image(
         image[image > 1] = 1
 
         # Return raw png
-        image = Image.fromArray((image * 65535).astype(np.uint16))
+        image = Image.fromarray((image * 65535).astype(np.uint16))
         filename = os.path.join(wd, f"scan{scan_id}_VLM_image_{title}.png")
         if dry_run:
             logger.info(f"Dry run: Not saving image to {filename}")

From 6d0543278e3104baaefba074f672eb2803aa4df8 Mon Sep 17 00:00:00 2001
From: Jun Aishima <jaishima@bnl.gov>
Date: Thu, 2 Apr 2026 13:28:34 -0400
Subject: [PATCH 11/12] remove unnecessary kwargs, set wd in function

---
 vlm_snapshot_exporter.py | 25 ++++---------------------
 1 file changed, 4 insertions(+), 21 deletions(-)

diff --git a/vlm_snapshot_exporter.py b/vlm_snapshot_exporter.py
index 7b56378..2c6833f 100644
--- a/vlm_snapshot_exporter.py
+++ b/vlm_snapshot_exporter.py
@@ -14,7 +14,7 @@ def vlm_image_exporter(ref, api_key=None, dry_run=False):
     logger.info(f"Looking for snapshots in scan {scan_id}.")
 
     export_vlm_image(
-        scan_id, overlay=True, raw_image=True, api_key=api_key, dry_run=dry_run
+        scan_id, api_key=api_key, dry_run=dry_run
     )
     logger.info(f"Finished exporting any snapshots in scan {scan_id}.")
 
@@ -22,27 +22,11 @@ def vlm_image_exporter(ref, api_key=None, dry_run=False):
 @task
 def export_vlm_image(
     scan_id,
-    wd=None,
-    overlay=True,
-    raw_image=True,
-    autoscale=True,
     api_key=None,
     dry_run=False,
 ):
     logger = get_run_logger()
 
-    # Pseudocode
-    # overlays == True
-    #       raw_images == True:
-    #           Saves both raw images and overlays
-    #       raw_images == False:
-    #           Saves only overlaid images
-    # overlays == False
-    #       raw_images == True:
-    #           Saves only raw images
-    #       raw_images == False:
-    #           raises RuntimeError
-
     # Initial checks
     # Does scan exist
     scan_id = int(scan_id)
@@ -54,10 +38,9 @@ def export_vlm_image(
         logger.info(warn_str)
         return
 
-    if wd is None:
-        proposal_id = h.start["proposal"]["proposal_id"]
-        cycle = h.start["cycle"]
-        wd = f"/nsls2/data/srx/proposals/{cycle}/pass-{proposal_id}/"
+    proposal_id = h.start["proposal"]["proposal_id"]
+    cycle = h.start["cycle"]
+    wd = f"/nsls2/data/srx/proposals/{cycle}/pass-{proposal_id}/"
 
     # Create sub-folder
     wd = f"{wd}vlm_snapshots/"

From 2d77f656c6087e5ccb13c4ee7cdf38971bec57af Mon Sep 17 00:00:00 2001
From: Jun Aishima <jaishima@bnl.gov>
Date: Thu, 2 Apr 2026 13:58:10 -0400
Subject: [PATCH 12/12] pre-commit lint fix

---
 vlm_snapshot_exporter.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/vlm_snapshot_exporter.py b/vlm_snapshot_exporter.py
index 2c6833f..4d146e5 100644
--- a/vlm_snapshot_exporter.py
+++ b/vlm_snapshot_exporter.py
@@ -13,9 +13,7 @@ def vlm_image_exporter(ref, api_key=None, dry_run=False):
     scan_id = get_run(ref, api_key=api_key).start["scan_id"]
     logger.info(f"Looking for snapshots in scan {scan_id}.")
 
-    export_vlm_image(
-        scan_id, api_key=api_key, dry_run=dry_run
-    )
+    export_vlm_image(scan_id, api_key=api_key, dry_run=dry_run)
     logger.info(f"Finished exporting any snapshots in scan {scan_id}.")