From b067b9dd393f8c0aeae7e1a87679db9a5f5dfd41 Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Thu, 13 Nov 2025 14:47:22 -0800 Subject: [PATCH 1/2] set camera --- cellpack/autopack/upy/simularium/simularium_helper.py | 2 +- cellpack/bin/simularium_converter.py | 2 +- examples/recipes/v2/spheres_in_a_box.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cellpack/autopack/upy/simularium/simularium_helper.py b/cellpack/autopack/upy/simularium/simularium_helper.py index 774439b17..bebc1be0e 100644 --- a/cellpack/autopack/upy/simularium/simularium_helper.py +++ b/cellpack/autopack/upy/simularium/simularium_helper.py @@ -1328,7 +1328,7 @@ def writeToFile(self, file_name, bb, recipe_name, version): n_subpoints[t][n] = 0 n += 1 - camera_z_position = box_size[2] if box_size[2] > 10 else 100.0 + camera_z_position = box_size[2] * 1.5 converted_data = TrajectoryData( meta_data=MetaData( box_size=np.array(box_size), diff --git a/cellpack/bin/simularium_converter.py b/cellpack/bin/simularium_converter.py index abe2c9726..53261ae5d 100644 --- a/cellpack/bin/simularium_converter.py +++ b/cellpack/bin/simularium_converter.py @@ -390,7 +390,7 @@ def main(): converter.fill_in_empty_fiber_data(time_point_index) if converter.debug: print("SUBPOINTS LENGTH", len(converter.subpoints[time_point_index])) - camera_z_position = box_size[2] if box_size[2] > 10 else 100.0 + camera_z_position = box_size[2] * 1.5 converted_data = TrajectoryData( meta_data=MetaData( box_size=np.array(box_size), diff --git a/examples/recipes/v2/spheres_in_a_box.json b/examples/recipes/v2/spheres_in_a_box.json index 5b2859beb..4f09db7e7 100644 --- a/examples/recipes/v2/spheres_in_a_box.json +++ b/examples/recipes/v2/spheres_in_a_box.json @@ -11,7 +11,7 @@ [ 1000, 1000, - 1500 + 1000 ] ], "objects": { From 4bdf12ed23afbab93fc009bf54f1d713f6ba3986 Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Thu, 20 Nov 2025 14:15:36 -0800 Subject: [PATCH 2/2] use max dimension --- cellpack/autopack/upy/simularium/simularium_helper.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/cellpack/autopack/upy/simularium/simularium_helper.py b/cellpack/autopack/upy/simularium/simularium_helper.py index bebc1be0e..bb7ad09ab 100644 --- a/cellpack/autopack/upy/simularium/simularium_helper.py +++ b/cellpack/autopack/upy/simularium/simularium_helper.py @@ -1328,7 +1328,9 @@ def writeToFile(self, file_name, bb, recipe_name, version): n_subpoints[t][n] = 0 n += 1 - camera_z_position = box_size[2] * 1.5 + # use max dimension to make sure camera captures entire scene + max_box_dimension = max(box_size) + camera_z_position = max_box_dimension * 2.5 converted_data = TrajectoryData( meta_data=MetaData( box_size=np.array(box_size),