From 2f05473258995a736f5d85f829bdf51d1acacd74 Mon Sep 17 00:00:00 2001
From: Peter Ercius <percius@lbl.gov>
Date: Fri, 30 Jan 2026 13:57:41 -0800
Subject: [PATCH 01/12] remove some logging. Reduce n_trials to 25

---
 operators/quantem-direct-ptycho/run.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/operators/quantem-direct-ptycho/run.py b/operators/quantem-direct-ptycho/run.py
index 25d243b7..12f8c1f4 100644
--- a/operators/quantem-direct-ptycho/run.py
+++ b/operators/quantem-direct-ptycho/run.py
@@ -114,11 +114,6 @@ def quantem_direct_ptycho(
         return None
 
     # --- 5. Perform Calculation ---
-    logger.info(
-        f"Scan {scan_number}: Triggering calculation after {accumulator.num_batches_added} messages."
-    )
-    logger.info(f"Accumulator finished: {accumulator.finished}")
-
     logger.info(f"Scan {scan_number}: Calculating ptycho images.")
 
     # Calculation parameters
@@ -234,7 +229,7 @@ def quantem_direct_ptycho(
                 aberration_coefs=opt_aberration_coefs,
                 rotation_angle=opt_rotation_angle,
                 deconvolution_kernel=deconvolution_kernel,
-                n_trials=50,
+                n_trials=25,
                 max_batch_size=10,
             )
         else:

From 86eeafe9d64b900e7cc529aa55a09654b0ce7be2 Mon Sep 17 00:00:00 2001
From: Peter Ercius <percius@lbl.gov>
Date: Fri, 30 Jan 2026 14:02:59 -0800
Subject: [PATCH 02/12] use int for defocus and defocus search range. This
 allows comparison inside run.py

---
 operators/quantem-direct-ptycho/operator.json | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/operators/quantem-direct-ptycho/operator.json b/operators/quantem-direct-ptycho/operator.json
index ab1d5c68..97a30851 100644
--- a/operators/quantem-direct-ptycho/operator.json
+++ b/operators/quantem-direct-ptycho/operator.json
@@ -63,11 +63,19 @@
     {  
       "name": "initial_defocus",
       "label": "STEM defocus",
-      "type": "float",
-      "default": "0.0",
+      "type": "int",
+      "default": "0",
       "description": "The STEM defocus in nm.",
       "required": false
     },
+    {  
+      "name": "defocus_search_range_nm",
+      "label": "Defocus search range",
+      "type": "int",
+      "default": "50",
+      "description": "The defocus search range in nanometers. Set to zero to disable defocus optimization.",
+      "required": false
+    },
     {  
       "name": "diffraction_rotation_angle",
       "label": "Diffraction pattern rotation angle",
@@ -92,14 +100,6 @@
       "description": "The upsampling factor for the final reconstruction.",
       "required": false
     },
-    {  
-      "name": "defocus_search_range_nm",
-      "label": "Defocus search range",
-      "type": "float",
-      "default": "50.0",
-      "description": "The defocus search range in nanometers. Unused if defocus is input.",
-      "required": false
-    },
     {  
       "name": "maximum_C12_magnitude_nm",
       "label": "Maximum C12 magnitude",

From a8e3c4e0e2d07fefc702da38e98be92b0cbf6e3c Mon Sep 17 00:00:00 2001
From: Peter Ercius <percius@lbl.gov>
Date: Fri, 30 Jan 2026 14:30:06 -0800
Subject: [PATCH 03/12] remove unused parameters

---
 operators/quantem-direct-ptycho/operator.json | 16 --------------
 operators/quantem-direct-ptycho/run.py        | 21 ++++++++++---------
 2 files changed, 11 insertions(+), 26 deletions(-)

diff --git a/operators/quantem-direct-ptycho/operator.json b/operators/quantem-direct-ptycho/operator.json
index 97a30851..75a90c26 100644
--- a/operators/quantem-direct-ptycho/operator.json
+++ b/operators/quantem-direct-ptycho/operator.json
@@ -20,22 +20,6 @@
     }
   ],
   "parameters": [
-    {
-      "name": "calculation_frequency",
-      "label": "Calculation Frequency",
-      "type": "int",
-      "default": "100",
-      "description": "Number of frames to accumulate before recalculating the center and emitting a BF image.",
-      "required": true
-    },
-    {
-      "name": "max_concurrent_scans",
-      "label": "Max Concurrent Scans",
-      "type": "int",
-      "default": "1",
-      "description": "Maximum number of scans to keep in memory simultaneously. Oldest scans are evicted when this limit is exceeded.",
-      "required": false
-    },
    {  
       "name": "accelerating_voltage",
       "label": "Accelerating voltage",
diff --git a/operators/quantem-direct-ptycho/run.py b/operators/quantem-direct-ptycho/run.py
index 12f8c1f4..578bb990 100644
--- a/operators/quantem-direct-ptycho/run.py
+++ b/operators/quantem-direct-ptycho/run.py
@@ -80,7 +80,7 @@ def quantem_direct_ptycho(
     scan_number = batch.header.scan_number
 
     # --- 2. Get or Create FrameAccumulator ---
-    max_concurrent_scans = int(parameters.get("max_concurrent_scans", 1))
+    max_concurrent_scans = 1  # TODO: remove this
 
     if scan_number not in accumulators:
         # Check if we need to evict old accumulators before creating new one
@@ -126,15 +126,21 @@ def quantem_direct_ptycho(
     upsampling_factor = parameters.get("upsampling_factor", 2)
 
     # Parameters for optimize_hyperparameters function
-    initial_defocus_nm = parameters.get(
-        "initial_defocus", None
-    )  # in nanometers, can be None
+    initial_defocus_nm = parameters.get("initial_defocus", 0)  # in nanometers
     if initial_defocus_nm is not None:
         initial_defocus_nm = initial_defocus_nm
         initial_defocus_A = initial_defocus_nm * 10  # convert to Angstroms
     else:
         initial_defocus_A = None
 
+    defocus_search_range_nm = parameters.get(
+        "defocus_search_range", 50
+    )  # in nanometers
+    defocus_search_range_A = defocus_search_range_nm * 10  # convert to Angstroms
+
+    if defocus_search_range_nm == 0:
+        defocus_search_range_A = None
+
     diffraction_rotation_angle = parameters.get(
         "diffraction_rotation_angle", None
     )  # in degrees, can be None
@@ -144,11 +150,6 @@ def quantem_direct_ptycho(
     else:
         rotation_angle = None
 
-    defocus_search_range_nm = parameters.get(
-        "defocus_search_range", 50
-    )  # in nanometers
-    defocus_search_range_A = defocus_search_range_nm * 10  # convert to Angstroms
-
     maximum_C12_magnitude_nm = parameters.get(
         "maximum_C12_magnitude", 10
     )  # in nanometers
@@ -181,7 +182,7 @@ def quantem_direct_ptycho(
 
     dset.sampling[0] = (
         probe_step_size * 10
-    )  ## convert to be Anggstrom for quantem. distiller will give nanometers.
+    )  ## convert to be Angstrom for quantem. distiller will give nanometers.
     dset.sampling[1] = probe_step_size * 10
     dset.units[0:2] = ["A", "A"]
 

From 77de16a1ebf1306e5fab0d0449dc29a86a8827da Mon Sep 17 00:00:00 2001
From: Peter Ercius <percius@lbl.gov>
Date: Fri, 30 Jan 2026 17:44:39 -0800
Subject: [PATCH 04/12] add bool parameters to enable optimization of
 diffraction_angle, defocus, and C12. Only search one side of focus based on
 the initial defocus.

---
 operators/quantem-direct-ptycho/operator.json | 48 ++++++----
 operators/quantem-direct-ptycho/run.py        | 93 +++++++++----------
 2 files changed, 78 insertions(+), 63 deletions(-)

diff --git a/operators/quantem-direct-ptycho/operator.json b/operators/quantem-direct-ptycho/operator.json
index 75a90c26..864d9ada 100644
--- a/operators/quantem-direct-ptycho/operator.json
+++ b/operators/quantem-direct-ptycho/operator.json
@@ -52,6 +52,14 @@
       "description": "The STEM defocus in nm.",
       "required": false
     },
+    {
+      "name": "optimize_defocus",
+      "label": "Optimize the defocus",
+      "type": "bool",
+      "default": true,
+      "description": "Use the optimization routine to optimize the defocus.",
+      "required": false
+    }
     {  
       "name": "defocus_search_range_nm",
       "label": "Defocus search range",
@@ -68,6 +76,30 @@
       "description": "The rotation of the diffraction pattern on the detector in degrees.",
       "required": false
     },
+    {
+      "name": "optimize_rotation_angle",
+      "label": "Optimize the rotation angle",
+      "type": "bool",
+      "default": false,
+      "description": "Use the optimization routine to optimize the rotation angle.",
+      "required": false
+    },
+    {  
+      "name": "maximum_C12_magnitude_nm",
+      "label": "Maximum C12 magnitude",
+      "type": "int",
+      "default": "2",
+      "description": "The maximum C12 magnitude in nanometers.",
+      "required": false
+    },
+    {
+      "name": "optimize_C12",
+      "label": "Optimize the C12",
+      "type": "bool",
+      "default": true,
+      "description": "Use the optimization routine to optimize the C12.",
+      "required": false
+    },
     {  
       "name": "crop_probes",
       "label": "Crop probes on each side",
@@ -84,14 +116,6 @@
       "description": "The upsampling factor for the final reconstruction.",
       "required": false
     },
-    {  
-      "name": "maximum_C12_magnitude_nm",
-      "label": "Maximum C12 magnitude",
-      "type": "int",
-      "default": "2",
-      "description": "The maximum C12 magnitude in nanometers.",
-      "required": false
-    },
     {  
       "name": "deconvolution_kernel",
       "label": "Deconvolution kernel",
@@ -100,14 +124,6 @@
       "options": ["parallax", "ssb", "icom"],
       "description": "The deconvolution kernel.",
       "required": false
-    },
-    {
-      "name": "use_optimization",
-      "label": "Use optimization routine",
-      "type": "bool",
-      "default": true,
-      "description": "Use the optimization routine with initial parameters.",
-      "required": false
     }
   ],
   "parallel_config": {
diff --git a/operators/quantem-direct-ptycho/run.py b/operators/quantem-direct-ptycho/run.py
index 578bb990..faf87198 100644
--- a/operators/quantem-direct-ptycho/run.py
+++ b/operators/quantem-direct-ptycho/run.py
@@ -117,49 +117,47 @@ def quantem_direct_ptycho(
     logger.info(f"Scan {scan_number}: Calculating ptycho images.")
 
     # Calculation parameters
-    probe_semiangle = parameters.get("probe_semiangle", 25.0)
     energy = parameters.get("accelerating_voltage", 300e3)
-    probe_step_size = parameters.get(
-        "probe_step_size", 0.1
-    )  # test data set: 0.14383155 nm
-    crop_probes = parameters.get("crop_probes", 0)
+    probe_semiangle = parameters.get("probe_semiangle", 25.0)
+    # test data set: 0.14383155 nm probe step size
+    probe_step_size_nm = parameters.get("probe_step_size", 0.1)
+    probe_step_size_A = probe_step_size_nm * 10
     upsampling_factor = parameters.get("upsampling_factor", 2)
 
-    # Parameters for optimize_hyperparameters function
-    initial_defocus_nm = parameters.get("initial_defocus", 0)  # in nanometers
-    if initial_defocus_nm is not None:
-        initial_defocus_nm = initial_defocus_nm
-        initial_defocus_A = initial_defocus_nm * 10  # convert to Angstroms
+    optimize_defocus = bool(parameters.get("optimize_defocus", True))
+    if optimize_defocus:
+        defocus_search_max_nm = parameters.get("defocus_search_range", 50)
+        defocus_search_max_A = defocus_search_max_nm * 10  # convert to Angstroms
     else:
-        initial_defocus_A = None
-
-    defocus_search_range_nm = parameters.get(
-        "defocus_search_range", 50
-    )  # in nanometers
-    defocus_search_range_A = defocus_search_range_nm * 10  # convert to Angstroms
-
-    if defocus_search_range_nm == 0:
-        defocus_search_range_A = None
-
-    diffraction_rotation_angle = parameters.get(
-        "diffraction_rotation_angle", None
-    )  # in degrees, can be None
-    if diffraction_rotation_angle is not None:
-        diffraction_rotation_angle = diffraction_rotation_angle
-        rotation_angle = diffraction_rotation_angle * np.pi / 180  # convert to radians
+        defocus_search_max_A = 0
+
+    initial_defocus_nm = parameters.get("initial_defocus", 0)
+    initial_defocus_A = initial_defocus_nm * 10
+
+    # Only search in one direction from initial guess
+    if initial_defocus_A > 0:
+        defocus_search_range_A = (0, defocus_search_max_A)
+    elif initial_defocus_A < 0:
+        defocus_search_range_A = (-defocus_search_max_A, 0)
     else:
-        rotation_angle = None
+        defocus_search_range_A = (-defocus_search_max_A, defocus_search_max_A)
 
-    maximum_C12_magnitude_nm = parameters.get(
-        "maximum_C12_magnitude", 10
-    )  # in nanometers
-    maximum_C12_magnitude_A = maximum_C12_magnitude_nm * 10  # convert to Angstroms
+    # in degrees
+    diffraction_rotation_angle_deg = parameters.get("diffraction_rotation_angle", 0)
+    rotation_angle = diffraction_rotation_angle_deg * np.pi / 180  # convert to radians
 
-    deconvolution_kernel = parameters.get("deconvolution_kernel", "parallax")
+    optimize_angle = bool(parameters.get("optimize_angle", False))
+
+    optimize_C12 = bool(parameters.get("optimize_C12", False))
+    if optimize_C12:
+        maximum_C12_magnitude_nm = parameters.get("maximum_C12_magnitude", 10)
+        maximum_C12_magnitude_A = maximum_C12_magnitude_nm * 10  # convert to Angstroms
+    else:
+        maximum_C12_magnitude_A = None
 
-    # Determine whether to use optimization or manual settings
-    use_optimization = bool(parameters.get("use_optimization", True))
+    deconvolution_kernel = parameters.get("deconvolution_kernel", "parallax")
 
+    crop_probes = parameters.get("crop_probes", 0)
     if crop_probes == 0:
         logger.info(f"Scan {scan_number}: No cropping of probes applied.")
         dense_data = accumulator[:, :-1, :, :].to_dense()  ## remove the flyback column
@@ -169,6 +167,7 @@ def quantem_direct_ptycho(
             crop_probes:-crop_probes, crop_probes : -crop_probes - 1, :, :
         ].to_dense()  ## crop the edges if needed and remove the flyback column
 
+    # Convert SparseArray to Dataset4dstem
     dset = em.datastructures.Dataset4dstem.from_array(array=dense_data)
     logger.debug(f"dense shape = {dense_data.shape}")
 
@@ -180,10 +179,7 @@ def quantem_direct_ptycho(
     dset.sampling[3] = probe_semiangle / probe_R
     dset.units[2:] = ["mrad", "mrad"]
 
-    dset.sampling[0] = (
-        probe_step_size * 10
-    )  ## convert to be Angstrom for quantem. distiller will give nanometers.
-    dset.sampling[1] = probe_step_size * 10
+    dset.sampling[0:2] = probe_step_size_A * 10
     dset.units[0:2] = ["A", "A"]
 
     logger.info(f"Scan {scan_number}: Start direct ptycho")
@@ -203,25 +199,28 @@ def quantem_direct_ptycho(
             rotation_angle=rotation_angle,  # need radians
         )
 
-        if use_optimization:
+        if optimize_C12 or optimize_angle or optimize_defocus:
             logger.info(f"Scan {scan_number}: Optimizing hyperparameters")
 
             # Build optimization aberration coefficients
             opt_aberration_coefs = {}
-            if initial_defocus_A is None:
+
+            if optimize_defocus:
                 opt_aberration_coefs["C10"] = OptimizationParameter(
-                    defocus_search_range_A, defocus_search_range_A
+                    defocus_search_range_A[0], defocus_search_range_A[1]
                 )
             else:
                 opt_aberration_coefs["C10"] = -initial_defocus_A
 
-            opt_aberration_coefs["C12"] = OptimizationParameter(
-                0, maximum_C12_magnitude_A
-            )
-            opt_aberration_coefs["phi12"] = OptimizationParameter(-np.pi / 2, np.pi / 2)
+            if optimize_C12:
+                opt_aberration_coefs["C12"] = OptimizationParameter(
+                    0, maximum_C12_magnitude_A
+                )
+                opt_aberration_coefs["phi12"] = OptimizationParameter(
+                    -np.pi / 2, np.pi / 2
+                )
 
-            # Build rotation angle optimization
-            if rotation_angle is None:
+            if optimize_angle:
                 opt_rotation_angle = OptimizationParameter(0, np.pi)
             else:
                 opt_rotation_angle = rotation_angle

From 07e3f38d5c93cfd519e6473666ab29ee721856bc Mon Sep 17 00:00:00 2001
From: Peter Ercius <percius@lbl.gov>
Date: Fri, 30 Jan 2026 17:50:11 -0800
Subject: [PATCH 05/12] fix json comma

---
 operators/quantem-direct-ptycho/operator.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/operators/quantem-direct-ptycho/operator.json b/operators/quantem-direct-ptycho/operator.json
index 864d9ada..d9507a69 100644
--- a/operators/quantem-direct-ptycho/operator.json
+++ b/operators/quantem-direct-ptycho/operator.json
@@ -59,7 +59,7 @@
       "default": true,
       "description": "Use the optimization routine to optimize the defocus.",
       "required": false
-    }
+    },
     {  
       "name": "defocus_search_range_nm",
       "label": "Defocus search range",

From 501aefc3fc24d247658ded98e320039a0e37e979 Mon Sep 17 00:00:00 2001
From: Peter Ercius <percius@lbl.gov>
Date: Fri, 30 Jan 2026 17:54:50 -0800
Subject: [PATCH 06/12] fix typos. Fix error where probe step size was x10
 twice

---
 operators/quantem-direct-ptycho/operator.json | 4 ++--
 operators/quantem-direct-ptycho/run.py        | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/operators/quantem-direct-ptycho/operator.json b/operators/quantem-direct-ptycho/operator.json
index d9507a69..33d1eb1c 100644
--- a/operators/quantem-direct-ptycho/operator.json
+++ b/operators/quantem-direct-ptycho/operator.json
@@ -61,7 +61,7 @@
       "required": false
     },
     {  
-      "name": "defocus_search_range_nm",
+      "name": "defocus_search_range",
       "label": "Defocus search range",
       "type": "int",
       "default": "50",
@@ -85,7 +85,7 @@
       "required": false
     },
     {  
-      "name": "maximum_C12_magnitude_nm",
+      "name": "maximum_C12_magnitude",
       "label": "Maximum C12 magnitude",
       "type": "int",
       "default": "2",
diff --git a/operators/quantem-direct-ptycho/run.py b/operators/quantem-direct-ptycho/run.py
index faf87198..b7382cac 100644
--- a/operators/quantem-direct-ptycho/run.py
+++ b/operators/quantem-direct-ptycho/run.py
@@ -146,7 +146,7 @@ def quantem_direct_ptycho(
     diffraction_rotation_angle_deg = parameters.get("diffraction_rotation_angle", 0)
     rotation_angle = diffraction_rotation_angle_deg * np.pi / 180  # convert to radians
 
-    optimize_angle = bool(parameters.get("optimize_angle", False))
+    optimize_angle = bool(parameters.get("optimize_rotation_angle", False))
 
     optimize_C12 = bool(parameters.get("optimize_C12", False))
     if optimize_C12:
@@ -179,7 +179,7 @@ def quantem_direct_ptycho(
     dset.sampling[3] = probe_semiangle / probe_R
     dset.units[2:] = ["mrad", "mrad"]
 
-    dset.sampling[0:2] = probe_step_size_A * 10
+    dset.sampling[0:2] = probe_step_size_A
     dset.units[0:2] = ["A", "A"]
 
     logger.info(f"Scan {scan_number}: Start direct ptycho")

From 14d3c5341781ff2b98508028d0bbc9ed8ce59f5d Mon Sep 17 00:00:00 2001
From: Peter Ercius <percius@lbl.gov>
Date: Mon, 2 Feb 2026 11:11:47 -0800
Subject: [PATCH 07/12] always use parallax for hyperparameter optimization

---
 operators/quantem-direct-ptycho/run.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/operators/quantem-direct-ptycho/run.py b/operators/quantem-direct-ptycho/run.py
index b7382cac..36560997 100644
--- a/operators/quantem-direct-ptycho/run.py
+++ b/operators/quantem-direct-ptycho/run.py
@@ -228,7 +228,7 @@ def quantem_direct_ptycho(
             direct_ptycho.optimize_hyperparameters(
                 aberration_coefs=opt_aberration_coefs,
                 rotation_angle=opt_rotation_angle,
-                deconvolution_kernel=deconvolution_kernel,
+                deconvolution_kernel="parallax",
                 n_trials=25,
                 max_batch_size=10,
             )

From aac6738cf4f7958439bdcde852e857ca116d27ea Mon Sep 17 00:00:00 2001
From: Peter Ercius <percius@lbl.gov>
Date: Mon, 2 Feb 2026 13:54:26 -0800
Subject: [PATCH 08/12] use only needed parameters.

---
 operators/quantem-direct-ptycho/operator.json | 50 +++++++------------
 1 file changed, 17 insertions(+), 33 deletions(-)

diff --git a/operators/quantem-direct-ptycho/operator.json b/operators/quantem-direct-ptycho/operator.json
index 33d1eb1c..b8976e2f 100644
--- a/operators/quantem-direct-ptycho/operator.json
+++ b/operators/quantem-direct-ptycho/operator.json
@@ -45,29 +45,21 @@
       "required": false
     },
     {  
-      "name": "initial_defocus",
-      "label": "STEM defocus",
+      "name": "defocus_search_range_min",
+      "label": "Defocus search range minimum",
       "type": "int",
       "default": "0",
-      "description": "The STEM defocus in nm.",
+      "description": "The defocus search range minimum in nanometers.",
       "required": false
     },
     {
-      "name": "optimize_defocus",
-      "label": "Optimize the defocus",
-      "type": "bool",
-      "default": true,
-      "description": "Use the optimization routine to optimize the defocus.",
-      "required": false
-    },
-    {  
-      "name": "defocus_search_range",
-      "label": "Defocus search range",
+      "name": "defocus_search_range_max",
+      "label": "Defocus search range maximum",
       "type": "int",
-      "default": "50",
-      "description": "The defocus search range in nanometers. Set to zero to disable defocus optimization.",
+      "default": "30",
+      "description": "The defocus search range maximum in nanometers.",
       "required": false
-    },
+    }
     {  
       "name": "diffraction_rotation_angle",
       "label": "Diffraction pattern rotation angle",
@@ -76,30 +68,14 @@
       "description": "The rotation of the diffraction pattern on the detector in degrees.",
       "required": false
     },
-    {
-      "name": "optimize_rotation_angle",
-      "label": "Optimize the rotation angle",
-      "type": "bool",
-      "default": false,
-      "description": "Use the optimization routine to optimize the rotation angle.",
-      "required": false
-    },
     {  
       "name": "maximum_C12_magnitude",
       "label": "Maximum C12 magnitude",
       "type": "int",
-      "default": "2",
+      "default": "10",
       "description": "The maximum C12 magnitude in nanometers.",
       "required": false
     },
-    {
-      "name": "optimize_C12",
-      "label": "Optimize the C12",
-      "type": "bool",
-      "default": true,
-      "description": "Use the optimization routine to optimize the C12.",
-      "required": false
-    },
     {  
       "name": "crop_probes",
       "label": "Crop probes on each side",
@@ -116,6 +92,14 @@
       "description": "The upsampling factor for the final reconstruction.",
       "required": false
     },
+    {  
+      "name": "n_trials",
+      "label": "Number of trials for hyperparameter optimization",
+      "type": "int",
+      "default": "25",
+      "description": "The number of trials for hyperparameter optimization.",
+      "required": false
+    },
     {  
       "name": "deconvolution_kernel",
       "label": "Deconvolution kernel",

From fc3071603fe292f90e53147d210344cda154d2ec Mon Sep 17 00:00:00 2001
From: Peter Ercius <percius@lbl.gov>
Date: Mon, 2 Feb 2026 13:58:44 -0800
Subject: [PATCH 09/12] add max_batch_size parameter to better manage memory

---
 operators/quantem-direct-ptycho/operator.json | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/operators/quantem-direct-ptycho/operator.json b/operators/quantem-direct-ptycho/operator.json
index b8976e2f..b3b01250 100644
--- a/operators/quantem-direct-ptycho/operator.json
+++ b/operators/quantem-direct-ptycho/operator.json
@@ -100,6 +100,14 @@
       "description": "The number of trials for hyperparameter optimization.",
       "required": false
     },
+    {
+      "name": "max_batch_size",
+      "label": "Maximum batch size",
+      "type": "int",
+      "default": "10",
+      "description": "The maximum batch size for processing frames. Reduce if you run out of GPU memory.",
+      "required": false
+    }
     {  
       "name": "deconvolution_kernel",
       "label": "Deconvolution kernel",

From d02a30b8508c7ad309aec2feff88815d8192610f Mon Sep 17 00:00:00 2001
From: Peter Ercius <percius@lbl.gov>
Date: Mon, 2 Feb 2026 14:17:50 -0800
Subject: [PATCH 10/12] fix up all the parameters

---
 operators/quantem-direct-ptycho/run.py | 122 +++++++++----------------
 1 file changed, 45 insertions(+), 77 deletions(-)

diff --git a/operators/quantem-direct-ptycho/run.py b/operators/quantem-direct-ptycho/run.py
index 36560997..060a33c8 100644
--- a/operators/quantem-direct-ptycho/run.py
+++ b/operators/quantem-direct-ptycho/run.py
@@ -80,7 +80,7 @@ def quantem_direct_ptycho(
     scan_number = batch.header.scan_number
 
     # --- 2. Get or Create FrameAccumulator ---
-    max_concurrent_scans = 1  # TODO: remove this
+    max_concurrent_scans = 1  # TODO: remove saving of old scans
 
     if scan_number not in accumulators:
         # Check if we need to evict old accumulators before creating new one
@@ -123,37 +123,22 @@ def quantem_direct_ptycho(
     probe_step_size_nm = parameters.get("probe_step_size", 0.1)
     probe_step_size_A = probe_step_size_nm * 10
     upsampling_factor = parameters.get("upsampling_factor", 2)
+    n_trials = parameters.get("n_trials", 25)
+    max_batch_size = parameters.get("max_batch_size", 10)
 
-    optimize_defocus = bool(parameters.get("optimize_defocus", True))
-    if optimize_defocus:
-        defocus_search_max_nm = parameters.get("defocus_search_range", 50)
-        defocus_search_max_A = defocus_search_max_nm * 10  # convert to Angstroms
-    else:
-        defocus_search_max_A = 0
-
-    initial_defocus_nm = parameters.get("initial_defocus", 0)
-    initial_defocus_A = initial_defocus_nm * 10
-
-    # Only search in one direction from initial guess
-    if initial_defocus_A > 0:
-        defocus_search_range_A = (0, defocus_search_max_A)
-    elif initial_defocus_A < 0:
-        defocus_search_range_A = (-defocus_search_max_A, 0)
-    else:
-        defocus_search_range_A = (-defocus_search_max_A, defocus_search_max_A)
+    defocus_search_min_nm = parameters.get("defocus_search_range_min", 50)
+    defocus_search_max_nm = parameters.get("defocus_search_range_max", 50)
+    defocus_search_min_A = defocus_search_min_nm * 10  # convert to Angstroms
+    defocus_search_max_A = defocus_search_max_nm * 10  # convert to Angstroms
+    # Need to convert signs and order because of different conventions in FEI and quantem
+    defocus_search_range_A = (-defocus_search_max_A, -defocus_search_min_A)
 
     # in degrees
     diffraction_rotation_angle_deg = parameters.get("diffraction_rotation_angle", 0)
     rotation_angle = diffraction_rotation_angle_deg * np.pi / 180  # convert to radians
 
-    optimize_angle = bool(parameters.get("optimize_rotation_angle", False))
-
-    optimize_C12 = bool(parameters.get("optimize_C12", False))
-    if optimize_C12:
-        maximum_C12_magnitude_nm = parameters.get("maximum_C12_magnitude", 10)
-        maximum_C12_magnitude_A = maximum_C12_magnitude_nm * 10  # convert to Angstroms
-    else:
-        maximum_C12_magnitude_A = None
+    maximum_C12_magnitude_nm = parameters.get("maximum_C12_magnitude", 10)
+    maximum_C12_magnitude_A = maximum_C12_magnitude_nm * 10  # convert to Angstroms
 
     deconvolution_kernel = parameters.get("deconvolution_kernel", "parallax")
 
@@ -184,76 +169,59 @@ def quantem_direct_ptycho(
 
     logger.info(f"Scan {scan_number}: Start direct ptycho")
     try:
-        # Initialize DirectPtychography with initial guesses
-        aberration_coefs = {}
-        if initial_defocus_A is not None:
-            aberration_coefs["C10"] = -initial_defocus_A  # Note the negative sign
+        # Initialize DirectPtychography
 
         direct_ptycho = DirectPtychography.from_dataset4d(
             dset,
             energy=energy,
             semiangle_cutoff=probe_semiangle,
             device=QUANTEM_DEVICE,
-            aberration_coefs=aberration_coefs if aberration_coefs else None,
-            max_batch_size=10,
+            aberration_coefs={},
+            max_batch_size=max_batch_size,
             rotation_angle=rotation_angle,  # need radians
         )
 
-        if optimize_C12 or optimize_angle or optimize_defocus:
-            logger.info(f"Scan {scan_number}: Optimizing hyperparameters")
-
-            # Build optimization aberration coefficients
-            opt_aberration_coefs = {}
-
-            if optimize_defocus:
-                opt_aberration_coefs["C10"] = OptimizationParameter(
-                    defocus_search_range_A[0], defocus_search_range_A[1]
-                )
-            else:
-                opt_aberration_coefs["C10"] = -initial_defocus_A
-
-            if optimize_C12:
-                opt_aberration_coefs["C12"] = OptimizationParameter(
-                    0, maximum_C12_magnitude_A
-                )
-                opt_aberration_coefs["phi12"] = OptimizationParameter(
-                    -np.pi / 2, np.pi / 2
-                )
-
-            if optimize_angle:
-                opt_rotation_angle = OptimizationParameter(0, np.pi)
-            else:
-                opt_rotation_angle = rotation_angle
-
-            direct_ptycho.optimize_hyperparameters(
-                aberration_coefs=opt_aberration_coefs,
-                rotation_angle=opt_rotation_angle,
-                deconvolution_kernel="parallax",
-                n_trials=25,
-                max_batch_size=10,
-            )
-        else:
-            logger.info(f"Scan {scan_number}: Using manual hyperparameter settings")
+        # Build optimization aberration coefficients
+        logger.info(f"Scan {scan_number}: Optimizing hyperparameters")
+        opt_aberration_coefs = {}
+        opt_aberration_coefs["C10"] = OptimizationParameter(
+            defocus_search_range_A[0], defocus_search_range_A[1]
+        )
+        opt_aberration_coefs["C12"] = OptimizationParameter(0, maximum_C12_magnitude_A)
+        opt_aberration_coefs["phi12"] = OptimizationParameter(-np.pi / 2, np.pi / 2)
+
+        # Optimize hyperparameters
+        direct_ptycho.optimize_hyperparameters(
+            aberration_coefs=opt_aberration_coefs,
+            deconvolution_kernel="parallax",
+            n_trials=n_trials,
+            max_batch_size=max_batch_size,
+        )
 
-        initial_parallax = direct_ptycho.reconstruct(
+        # Do reconstruction
+        logger.info(f"Scan {scan_number}: Starting reconstruction")
+        direct_ptycho.reconstruct(
             deconvolution_kernel=deconvolution_kernel,
             upsampling_factor=upsampling_factor,
-            max_batch_size=10,
+            max_batch_size=max_batch_size,
         )
 
         # Process and return result
         logger.info(f"Scan {scan_number}: Reconstruction done")
-        output_bytes = initial_parallax.obj.tobytes()
+        output_bytes = direct_ptycho.obj.tobytes()
         output_meta = {
             "scan_number": scan_number,
-            "shape": initial_parallax.obj.shape,
-            "dtype": str(initial_parallax.obj.dtype),
+            "shape": direct_ptycho.obj.shape,
+            "dtype": str(direct_ptycho.obj.dtype),
             "source_operator": "quantem-direct-ptycho",
-            "direct_ptycho_params": {'C12': direct_ptycho.hyperparameter_state.optimized_aberrations['C12'],
-                                     'phi12': direct_ptycho.hyperparameter_state.optimized_aberrations['phi12'],
-                                    'C10': -direct_ptycho.aberration_coefs['C10'],
-                                    'rotation_angle': direct_ptycho.rotation_angle,
-                                    },
+            "direct_ptycho_params": {
+                "C12": direct_ptycho.hyperparameter_state.optimized_aberrations["C12"],
+                "phi12": direct_ptycho.hyperparameter_state.optimized_aberrations[
+                    "phi12"
+                ],
+                "C10": -direct_ptycho.aberration_coefs["C10"],
+                "rotation_angle": direct_ptycho.rotation_angle,
+            },
         }
         header = MessageHeader(subject=MessageSubject.BYTES, meta=output_meta)
         return BytesMessage(header=header, data=output_bytes)

From e2298930a7a4694de5fbe5378ef82ace48d4afd9 Mon Sep 17 00:00:00 2001
From: Peter Ercius <percius@lbl.gov>
Date: Mon, 2 Feb 2026 14:24:54 -0800
Subject: [PATCH 11/12] fix json commas

---
 operators/quantem-direct-ptycho/operator.json | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/operators/quantem-direct-ptycho/operator.json b/operators/quantem-direct-ptycho/operator.json
index b3b01250..74892346 100644
--- a/operators/quantem-direct-ptycho/operator.json
+++ b/operators/quantem-direct-ptycho/operator.json
@@ -1,6 +1,6 @@
 {
   "id": "17460a60-01ac-4144-aa32-126bd62667aa",
-  "label": "quantem direct ptycho",
+  "label": "quantem direct ptycho 2",
   "description": "Use quantem to calculate direct ptychography reconstructions from counted data.",
   "image": "ghcr.io/nersc/interactem/quantem-direct-ptycho:latest",
   "inputs": [
@@ -59,7 +59,7 @@
       "default": "30",
       "description": "The defocus search range maximum in nanometers.",
       "required": false
-    }
+    },
     {  
       "name": "diffraction_rotation_angle",
       "label": "Diffraction pattern rotation angle",
@@ -107,7 +107,7 @@
       "default": "10",
       "description": "The maximum batch size for processing frames. Reduce if you run out of GPU memory.",
       "required": false
-    }
+    },
     {  
       "name": "deconvolution_kernel",
       "label": "Deconvolution kernel",

From 5f0a225bcf915feba02ce22b19ba8497b00c558a Mon Sep 17 00:00:00 2001
From: Peter Ercius <percius@lbl.gov>
Date: Mon, 2 Feb 2026 14:44:41 -0800
Subject: [PATCH 12/12] remove naming typo

---
 operators/quantem-direct-ptycho/operator.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/operators/quantem-direct-ptycho/operator.json b/operators/quantem-direct-ptycho/operator.json
index 74892346..5abc3021 100644
--- a/operators/quantem-direct-ptycho/operator.json
+++ b/operators/quantem-direct-ptycho/operator.json
@@ -1,6 +1,6 @@
 {
   "id": "17460a60-01ac-4144-aa32-126bd62667aa",
-  "label": "quantem direct ptycho 2",
+  "label": "quantem direct ptycho",
   "description": "Use quantem to calculate direct ptychography reconstructions from counted data.",
   "image": "ghcr.io/nersc/interactem/quantem-direct-ptycho:latest",
   "inputs": [