AMS-BP 0.4.0__py3-none-any.whl → 0.4.22__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- AMS_BP/__init__.py +1 -1
- AMS_BP/gui/README.md +40 -36
- AMS_BP/gui/widgets/molecule_config_widget.py +3 -3
- {ams_bp-0.4.0.dist-info → ams_bp-0.4.22.dist-info}/METADATA +11 -29
- {ams_bp-0.4.0.dist-info → ams_bp-0.4.22.dist-info}/RECORD +8 -8
- {ams_bp-0.4.0.dist-info → ams_bp-0.4.22.dist-info}/WHEEL +0 -0
- {ams_bp-0.4.0.dist-info → ams_bp-0.4.22.dist-info}/entry_points.txt +0 -0
- {ams_bp-0.4.0.dist-info → ams_bp-0.4.22.dist-info}/licenses/LICENSE +0 -0
AMS_BP/__init__.py
CHANGED
AMS_BP/gui/README.md
CHANGED
|
@@ -6,12 +6,12 @@ The AMS-BP GUI provides a user-friendly interface for constructing and validatin
|
|
|
6
6
|
|
|
7
7
|
This GUI supports:
|
|
8
8
|
|
|
9
|
-
A template-based configuration builder for quick setup.
|
|
10
|
-
A visual editor for each simulation parameter block (cells, molecules, fluorophores, lasers, etc.).
|
|
11
|
-
Interactive help sections for each tab.
|
|
12
|
-
Simulation execution using prebuilt configs.
|
|
13
|
-
Napari integration for visualization of resulting microscopy data.
|
|
14
|
-
Packaging of simulation logs for easy sharing.
|
|
9
|
+
- A template-based configuration builder for quick setup.
|
|
10
|
+
- A visual editor for each simulation parameter block (cells, molecules, fluorophores, lasers, etc.).
|
|
11
|
+
- Interactive help sections for each tab.
|
|
12
|
+
- Simulation execution using prebuilt configs.
|
|
13
|
+
- Napari integration for visualization of resulting microscopy data.
|
|
14
|
+
- Packaging of simulation logs for easy sharing.
|
|
15
15
|
|
|
16
16
|
## Launching the GUI
|
|
17
17
|
|
|
@@ -23,55 +23,59 @@ run_AMS_BP gui
|
|
|
23
23
|
### Main Window
|
|
24
24
|
The main window (MainWindow) acts as the launchpad for:
|
|
25
25
|
|
|
26
|
-
Configuration Builder — Launches a template selector and opens a full editor.
|
|
27
|
-
Run Simulation from Config — Lets you pick a .toml file and start the simulation.
|
|
28
|
-
Visualize Microscopy Data — Opens TIFF and other images in a Napari viewer.
|
|
29
|
-
Package Logs for Sharing — Archives a run_* folder into a .zip.
|
|
26
|
+
- Configuration Builder — Launches a template selector and opens a full editor.
|
|
27
|
+
- Run Simulation from Config — Lets you pick a .toml file and start the simulation.
|
|
28
|
+
- Visualize Microscopy Data — Opens TIFF and other images in a Napari viewer.
|
|
29
|
+
- Package Logs for Sharing — Archives a run_* folder into a .zip.
|
|
30
|
+
|
|
30
31
|
#### Configuration Editor
|
|
31
32
|
Once a template is selected, the ConfigEditor is launched. It contains:
|
|
32
33
|
|
|
33
|
-
A dropdown navigation system replacing traditional tabs.
|
|
34
|
-
A floating tab counter and preview/save buttons.
|
|
35
|
-
A help button per section (reads *.md files from help_docs/).
|
|
36
|
-
Live validation using internal config models (convertconfig.py).
|
|
34
|
+
- A dropdown navigation system replacing traditional tabs.
|
|
35
|
+
- A floating tab counter and preview/save buttons.
|
|
36
|
+
- A help button per section (reads *.md files from help_docs/).
|
|
37
|
+
- Live validation using internal config models (convertconfig.py).
|
|
38
|
+
|
|
37
39
|
##### Tabs & Widgets
|
|
38
40
|
Each configuration section is implemented as a modular PyQt widget, including:
|
|
39
41
|
|
|
40
|
-
GlobalConfigWidget
|
|
41
|
-
CellConfigWidget
|
|
42
|
-
MoleculeConfigWidget
|
|
43
|
-
FluorophoreConfigWidget
|
|
44
|
-
CondensateConfigWidget
|
|
45
|
-
LaserConfigWidget
|
|
46
|
-
ExperimentConfigWidget
|
|
47
|
-
...and more
|
|
42
|
+
- GlobalConfigWidget
|
|
43
|
+
- CellConfigWidget
|
|
44
|
+
- MoleculeConfigWidget
|
|
45
|
+
- FluorophoreConfigWidget
|
|
46
|
+
- CondensateConfigWidget
|
|
47
|
+
- LaserConfigWidget
|
|
48
|
+
- ExperimentConfigWidget
|
|
49
|
+
- ...and more
|
|
50
|
+
|
|
48
51
|
Each widget supports:
|
|
49
52
|
|
|
50
|
-
get_data() → Extract validated dictionary data
|
|
51
|
-
set_data(data: dict) → Load existing config into the UI
|
|
52
|
-
validate() → Validate using backend logic
|
|
53
|
-
get_help_path() → Load the corresponding markdown help page
|
|
53
|
+
- get_data() → Extract validated dictionary data
|
|
54
|
+
- set_data(data: dict) → Load existing config into the UI
|
|
55
|
+
- validate() → Validate using backend logic
|
|
56
|
+
- get_help_path() → Load the corresponding markdown help page
|
|
54
57
|
|
|
55
58
|
#### Running a Simulation
|
|
56
59
|
|
|
57
60
|
Once you've completed the config file setup via the GUI:
|
|
58
61
|
|
|
59
|
-
Click "Preview Configuration TOML" to confirm contents.
|
|
60
|
-
Click "Ready to Save Configuration" and choose a .toml path.
|
|
61
|
-
Return to the main window, click "Run Simulation from Config".
|
|
62
|
-
Simulation will launch in a background thread and print logs to a live window.
|
|
63
|
-
Once done, results will be saved in a run_*/ folder.
|
|
62
|
+
- Click "Preview Configuration TOML" to confirm contents.
|
|
63
|
+
- Click "Ready to Save Configuration" and choose a .toml path.
|
|
64
|
+
- Return to the main window, click "Run Simulation from Config".
|
|
65
|
+
- Simulation will launch in a background thread and print logs to a live window.
|
|
66
|
+
- Once done, results will be saved in a run_*/ folder.
|
|
64
67
|
|
|
65
68
|
#### Viewing Results
|
|
66
69
|
|
|
67
|
-
Click "Visualize Microscopy Data (Napari)"
|
|
68
|
-
Select any .tif, .tiff, .nd2, or .zarr file
|
|
70
|
+
- Click "Visualize Microscopy Data (Napari)"
|
|
71
|
+
- Select any .tif, .tiff, .nd2, or .zarr file
|
|
72
|
+
|
|
69
73
|
The data will be loaded into a new Napari viewer session
|
|
70
74
|
|
|
71
75
|
#### Packaging Logs
|
|
72
76
|
|
|
73
77
|
To share or archive a completed simulation:
|
|
74
78
|
|
|
75
|
-
Click "Package Logs for Sharing".
|
|
76
|
-
Select the run_* folder you want.
|
|
77
|
-
Choose a destination for the .zip file.
|
|
79
|
+
- Click "Package Logs for Sharing".
|
|
80
|
+
- Select the run_* folder you want.
|
|
81
|
+
- Choose a destination for the .zip file.
|
|
@@ -235,6 +235,9 @@ class MoleculeConfigWidget(QWidget):
|
|
|
235
235
|
}
|
|
236
236
|
self.molecule_type_widgets[i].set_data(type_data)
|
|
237
237
|
|
|
238
|
+
def get_help_path(self) -> Path:
|
|
239
|
+
return Path(__file__).parent.parent / "help_docs" / "molecule_help.md"
|
|
240
|
+
|
|
238
241
|
|
|
239
242
|
class MoleculeTypeWidget(QWidget):
|
|
240
243
|
def __init__(self, type_index):
|
|
@@ -709,6 +712,3 @@ class TransitionMatrixWidget(QWidget):
|
|
|
709
712
|
for i in range(size):
|
|
710
713
|
for j in range(min(size, len(matrix[i]))):
|
|
711
714
|
self.spinboxes[i][j].setValue(matrix[i][j])
|
|
712
|
-
|
|
713
|
-
def get_help_path(self) -> Path:
|
|
714
|
-
return Path(__file__).parent.parent / "help_docs" / "molecule_help.md"
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.4
|
|
2
2
|
Name: AMS_BP
|
|
3
|
-
Version: 0.4.
|
|
3
|
+
Version: 0.4.22
|
|
4
4
|
Summary: Advanced Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar
|
|
5
5
|
Project-URL: Documentation, https://joemans3.github.io/AMS_BP/
|
|
6
6
|
Project-URL: Source code, https://github.com/joemans3/AMS_BP
|
|
@@ -63,31 +63,29 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
|
|
|
63
63
|
|
|
64
64
|
|
|
65
65
|
### ***Installing the CLI tool using UV***
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
66
|
1. [Install UV](https://docs.astral.sh/uv/getting-started/installation/).
|
|
71
67
|
2. Run the command:
|
|
72
68
|
```bash
|
|
73
69
|
uv tool install AMS_BP
|
|
74
70
|
```
|
|
75
|
-
3. You will have access to
|
|
71
|
+
3. You will have access to three CLI commands (using the uv interface):
|
|
76
72
|
- `run_AMS_BP runsim` : This is the main entry point for the simulation. (see `run_AMS_BP runsim --help` for more details)
|
|
77
73
|
- `run_AMS_BP config` : This is a helper tool to generate a template config file for the simulation. (see `run_AMS_BP config --help` for more details)
|
|
74
|
+
- `run_AMS_BP gui` : to start the GUI. See [GUI Documentation](./src/AMS_BP/gui/README.md)
|
|
78
75
|
- Note: using `run_AMS_BP --help` will show you all the available commands.
|
|
79
76
|
4. You can now use these tools (they are isolated in their own env created by uv, which is cool).
|
|
80
77
|
|
|
81
78
|
### ***PyPi***
|
|
82
79
|
|
|
83
|
-
1.
|
|
80
|
+
1. If using pip, make sure the environment is python >= 3.12
|
|
81
|
+
2. Run:
|
|
84
82
|
```bash
|
|
85
83
|
pip install AMS_BP
|
|
86
84
|
```
|
|
87
85
|
|
|
88
86
|
## Command Line Interface
|
|
89
87
|
|
|
90
|
-
AMS-BP provides a command-line interface with
|
|
88
|
+
AMS-BP provides a command-line interface with three main commands:
|
|
91
89
|
|
|
92
90
|
```bash
|
|
93
91
|
# Generate a default configuration file
|
|
@@ -111,10 +109,10 @@ In addition to the CLI and programmatic API, AMS-BP comes with a graphical inter
|
|
|
111
109
|
### Main GUI Features
|
|
112
110
|
The GUI provides the following tools from a single interface:
|
|
113
111
|
|
|
114
|
-
**Create Configuration File** — Launches the visual configuration builder
|
|
115
|
-
**Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
|
|
116
|
-
**Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
|
|
117
|
-
**Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
|
|
112
|
+
- **Create Configuration File** — Launches the visual configuration builder
|
|
113
|
+
- **Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
|
|
114
|
+
- **Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
|
|
115
|
+
- **Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
|
|
118
116
|
|
|
119
117
|
### Launch the GUI
|
|
120
118
|
To start the GUI, run:
|
|
@@ -123,23 +121,7 @@ To start the GUI, run:
|
|
|
123
121
|
|
|
124
122
|
run_AMS_BP gui
|
|
125
123
|
```
|
|
126
|
-
|
|
127
|
-
Clicking "Create Configuration File" opens a template selector where you can choose a preconfigured simulation (with preview images), and then visually edit all configuration options through dedicated tabs.
|
|
128
|
-
|
|
129
|
-
Each section of the configuration is editable via structured UI forms, with contextual help and validation. Tabs include:
|
|
130
|
-
|
|
131
|
-
- Global/Cell/Molecule/Condensate/Fluorophore parameters
|
|
132
|
-
- Laser and optical configuration
|
|
133
|
-
- Camera and channel settings
|
|
134
|
-
- Experiment setup (e.g., z-stack vs time-series)
|
|
135
|
-
Once ready, click "Preview Configuration TOML" to inspect the final file, and "Save" to export.
|
|
136
|
-
|
|
137
|
-
#### Running Simulations from GUI
|
|
138
|
-
Clicking "Run Simulation from Config" lets you select any .toml configuration file. A real-time log viewer shows progress, and outputs are saved in a structured AMS_runs/run_*/ directory.
|
|
139
|
-
|
|
140
|
-
#### Sharing Logs
|
|
141
|
-
Run into an issue? Use the packge logs button to select the logs corresponding to the simulation you just ran, save them and send them over to us! It will help you diagnose the issue!
|
|
142
|
-
|
|
124
|
+
For detailed walkthrough see the [GUI Documentation](./src/AMS_BP/gui/README.md).
|
|
143
125
|
## Configuration File
|
|
144
126
|
|
|
145
127
|
The configuration file (sim_config.toml) is divided into several key sections:
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
AMS_BP/__init__.py,sha256=
|
|
1
|
+
AMS_BP/__init__.py,sha256=rV2K-9LYovKnN36znkN8Va6qfaDhXAeytS0ws77n8mU,327
|
|
2
2
|
AMS_BP/main_cli.py,sha256=DpRzWDsmI0nJvrzJj58F9k1k5ShSj8pCT7N0oH-_8BU,5786
|
|
3
3
|
AMS_BP/run_sim_util.py,sha256=UQr0l9rbtTmzuuWXjkIaTQV-ETO5AqyXRwflF6U2WYs,2415
|
|
4
4
|
AMS_BP/sim_config.toml,sha256=G0wW9qsxciZA1Y0Zm6YgZ00ZDBEBBLw_XXq4gsVRjSY,11778
|
|
@@ -13,7 +13,7 @@ AMS_BP/configio/experiments.py,sha256=HdfaSi0gPPJ_wLF87XcW5ICja19Uezx7-ygFEwNzi3
|
|
|
13
13
|
AMS_BP/configio/saving.py,sha256=596QgAadV32rzsN4B2FngGFcBWCzCDnLFN-qtQsv3bM,857
|
|
14
14
|
AMS_BP/groundtruth_generators/__init__.py,sha256=UPVmhiB81OfyqAes5LoN-n6XgQuBCYCqRPAGd2jpMfc,99
|
|
15
15
|
AMS_BP/groundtruth_generators/nuclearporecomplexes.py,sha256=1aBcWltsKo0OGd7A9GfuEZ3azQBx5SzpjrSLLMXuYn8,2518
|
|
16
|
-
AMS_BP/gui/README.md,sha256=
|
|
16
|
+
AMS_BP/gui/README.md,sha256=z2XreAPQeeFmKSXbhsa2kznHbk-YbLD55-VPWikNQp4,2778
|
|
17
17
|
AMS_BP/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
|
|
18
18
|
AMS_BP/gui/configuration_window.py,sha256=d-eEz099-LWSn0_O8ZKn1425jkMAxoAFW4-BZ3qW90c,12606
|
|
19
19
|
AMS_BP/gui/help_window.py,sha256=Jn844Vez7ULC1VGKb4iGgRvuw3wPTd0pcyRv7VWbeV4,790
|
|
@@ -46,7 +46,7 @@ AMS_BP/gui/widgets/flurophore_config_widget.py,sha256=Bri9TttiYM7eBkrcxLVjjvhein
|
|
|
46
46
|
AMS_BP/gui/widgets/general_config_widget.py,sha256=YbnE11TnWZBgb-xqKWM00p8RdSp-9eTbwTZ9mikPvZc,1321
|
|
47
47
|
AMS_BP/gui/widgets/global_config_widget.py,sha256=6X-NrBz5qc2mfDnH0kBGQKTgBaI3hqaaOAMpegFM7hs,4881
|
|
48
48
|
AMS_BP/gui/widgets/laser_config_widget.py,sha256=gtaZdFsPh8Zai03IoyhSp95hXa6biAoFmhJMaSe38XM,8737
|
|
49
|
-
AMS_BP/gui/widgets/molecule_config_widget.py,sha256=
|
|
49
|
+
AMS_BP/gui/widgets/molecule_config_widget.py,sha256=kvN_8JYe-rBJxfNgy0v7yRjT-RuT1KWMs_m0l6-sK1c,27789
|
|
50
50
|
AMS_BP/gui/widgets/output_config_widget.py,sha256=pExiAHIHs0-J-dY2lZtfB0ei9oNjZIJKDQtWDSjFZOY,2105
|
|
51
51
|
AMS_BP/gui/widgets/psf_config_widget.py,sha256=75ggeolYI_Sbn5LD_hUGY3S4Z9uRkJGtzZhb79NgsY4,4534
|
|
52
52
|
AMS_BP/gui/widgets/utility_widgets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
|
|
@@ -96,8 +96,8 @@ AMS_BP/utils/decorators.py,sha256=4qFdvzPJne0dhkhD1znPxRln1Rfr5NX8rdcCDcbATRU,62
|
|
|
96
96
|
AMS_BP/utils/errors.py,sha256=7BOd-L4_YeKmWn3Q4EOdTnNF3Bj_exDa3eg5X0yCZrc,759
|
|
97
97
|
AMS_BP/utils/maskMaker.py,sha256=2ca3n2nc8rFtUh1LurKXOJJsUmhrOpWbRnVX7fjRVvs,335
|
|
98
98
|
AMS_BP/utils/util_functions.py,sha256=9Qlr4kjY04fObktR8TrzB0IgoG1yXtcmxPRX9AN34mM,9671
|
|
99
|
-
ams_bp-0.4.
|
|
100
|
-
ams_bp-0.4.
|
|
101
|
-
ams_bp-0.4.
|
|
102
|
-
ams_bp-0.4.
|
|
103
|
-
ams_bp-0.4.
|
|
99
|
+
ams_bp-0.4.22.dist-info/METADATA,sha256=WQtOOw8Wz5IsbSojZNxRkzVZzCy_cQHFN4HHTxzaezw,9592
|
|
100
|
+
ams_bp-0.4.22.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
|
|
101
|
+
ams_bp-0.4.22.dist-info/entry_points.txt,sha256=06NS85P4dz6vosMOKXHfx8l7gK9WXBZxuwjl55XfT2c,65
|
|
102
|
+
ams_bp-0.4.22.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
|
|
103
|
+
ams_bp-0.4.22.dist-info/RECORD,,
|
|
File without changes
|
|
File without changes
|
|
File without changes
|