diff --git a/analysis.ipynb b/analysis.ipynb
index 6ef876e5ad0b19af4b38e40b8bc76cc7f61672fb..586a14ddc60189a8868ca5aecb9903014205c025 100644
--- a/analysis.ipynb
+++ b/analysis.ipynb
@@ -2,20 +2,27 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
- "%run \"functions.py\"\n",
"%matplotlib inline\n",
"\n",
+ "import os\n",
+ "\n",
"import ipywidgets as widgets\n",
"from ipywidgets import interactive, fixed, HBox, VBox\n",
"from ipyfilechooser import FileChooser\n",
"from IPython.display import HTML, Markdown, display, clear_output\n",
"\n",
- "def printmd(string):\n",
- " display(Markdown(string))"
+ "import manipylator\n",
+ "import manipylator.utils as utils \n",
+ "import manipylator.gui as gui\n",
+ "from manipylator.utils import printmd \n",
+ "from manipylator.analysis import tune_detect_bead\n",
+ "from manipylator.controller import Controller, get_stage_prop\n",
+ "\n",
+ "cwd = os.getcwd()"
]
},
{
@@ -27,7 +34,7 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 21,
"metadata": {},
"outputs": [
{
@@ -57,7 +64,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "68f8d68620004dfd8378451cd71b4f65",
+ "model_id": "a24127a5a5b445ffb61b45cf20a874fe",
"version_major": 2,
"version_minor": 0
},
@@ -79,7 +86,7 @@
},
{
"cell_type": "code",
- "execution_count": 138,
+ "execution_count": 23,
"metadata": {},
"outputs": [
{
@@ -97,12 +104,12 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "3a64141e9ab549a4bd448b2cb9d4ac18",
+ "model_id": "0bf65887ccf144a9a7d9e31c5a968559",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
- "FileChooser(path='/Users/amichaut/Desktop/selected_spheroids', filename='', title='HTML(value='', layout=Layou…"
+ "FileChooser(path='/Users/amichaut/Desktop', filename='', title='HTML(value='', layout=Layout(display='none'))'…"
]
},
"metadata": {},
@@ -219,7 +226,7 @@
"chirp_wid = widgets.Button(value=True, description=description)\n",
"\n",
"def make_chirp_info(obj):\n",
- " write_dict(exp_chirp,info_fn)\n",
+ " utils.write_dict(exp_chirp,info_fn)\n",
" \n",
"chirp_wid.on_click(make_chirp_info)\n",
"\n",
@@ -228,7 +235,7 @@
"PID_wid = widgets.Button(value=True, description=description)\n",
"\n",
"def make_PID_info(obj):\n",
- " write_dict(exp_PID,info_fn)\n",
+ " utils.write_dict(exp_PID,info_fn)\n",
" \n",
"PID_wid.on_click(make_PID_info)\n",
"\n",
@@ -237,7 +244,7 @@
"sweep_wid = widgets.Button(value=True, description=description)\n",
"\n",
"def make_sweep_info(obj):\n",
- " write_dict(exp_sweep,info_fn)\n",
+ " utils.write_dict(exp_sweep,info_fn)\n",
" \n",
"sweep_wid.on_click(make_sweep_info)\n",
"\n",
@@ -317,7 +324,7 @@
"image = stack[0]\n",
"h,w = image.shape\n",
"\n",
- "interactive_plot_param = interactive(select_ROI,\n",
+ "interactive_plot_param = interactive(utils.select_ROI,\n",
" x_range=widgets.IntRangeSlider(min=0,max=w,value=[0,w],continuous_update=False),\n",
" y_range=widgets.IntRangeSlider(min=0,max=h,value=[0,h],continuous_update=False),\n",
" intensity_range=widgets.IntRangeSlider(min=0,max=255,value=[0,255],continuous_update=False),\n",
@@ -1125,7 +1132,7 @@
"\n",
"# def make_flow_info(obj):\n",
"# exp_flow['tip_radius'] = np.sqrt(exp_flow['contact_area']/np.pi)/lengthscale\n",
- "# write_dict(exp_flow,osp.join(exp_flow['exp_dir'],'info.csv'))\n",
+ "# utils.write_dict(exp_flow,osp.join(exp_flow['exp_dir'],'info.csv'))\n",
" \n",
"# flow_wid.on_click(make_flow_info)"
]
diff --git a/manipylator/gui.py b/manipylator/gui.py
index 0ba3b00e8a554a6476952063f34dab391df802b9..c7853c19df6e3f542893d7cc317115166c5ce357 100644
--- a/manipylator/gui.py
+++ b/manipylator/gui.py
@@ -53,10 +53,31 @@ def printmd(string):
display(Markdown(string))
+def generate_show_pos(controller,output):
+ """
+ A function wrapper that generates a function to be passed to Widget on_click method
+ controller: controller.Controller object
+ output: ipywidgets.Output object
+ """
+
+ def show_pos(obj):
+ """
+ a function used to show the stage position when button clicked
+ """
+ output.clear_output()
+ pos = controller.get_pos(print_pos=False)
+ with output:
+ print('raw position = {} um\n'.format(pos))
+ print('transformed position = {} um\n'.format(controller.stage_pos))
+
+ return show_pos
+
+
+
def make_basic_dashboard(controller_dict, virtual):
"""
Make a dashboard to control the position and the servo of the connected controllers
- controller_dict: dict of Controller object
+ controller_dict: dict of controller.Controller object
virtual: bool if True controller are virtual
"""
@@ -98,41 +119,9 @@ def make_basic_dashboard(controller_dict, virtual):
# show position button
out = widgets.Output() # output to display position
-
- ### !!! quick and dirty solution that needs to be better addressed !!!
- ### prevent show_pos to be updated by the loop by giving it another name
- ### works only for 2 controllers
- if i == 0:
- def show_pos_0(obj):
- """
- a function used to show the stage position when button clicked
- """
- out = out_list[0]
- controller = controller_list[0]
- out.clear_output()
- pos = controller.get_pos(print_pos=False)
- with out:
- print('raw position = {} um\n'.format(pos))
- print('transformed position = {} um\n'.format(controller.stage_pos))
- elif i == 1:
- def show_pos_1(obj):
- """
- a function used to show the stage position when button clicked
- """
- out = out_list[1]
- controller = controller_list[1]
- out.clear_output()
- pos = controller.get_pos(print_pos=False)
- with out:
- print('raw position = {} um\n'.format(pos))
- print('transformed position = {} um\n'.format(controller.stage_pos))
-
- pos_wid = widgets.Button(value=True, description='Show position')
-
- if i == 0:
- pos_wid.on_click(show_pos_0)
- elif i == 1:
- pos_wid.on_click(show_pos_1)
+ pos_wid = widgets.Button(value=True, description='Show position') # button widget
+ show_pos = generate_show_pos(controller,out) # function to show position when button click
+ pos_wid.on_click(show_pos)
# store widgets, outputs and labels
diff --git a/stage_controler.ipynb b/stage_controler.ipynb
index bcf36eade706509e8d8fe09c6b6d12cc1fa5f011..d40e0f53867b057531b7a9421ee18a7d01e471e8 100755
--- a/stage_controler.ipynb
+++ b/stage_controler.ipynb
@@ -74,7 +74,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "ac1bf6070c7f422db84ba9dd637998e5",
+ "model_id": "37fa5a36f5b048a9b323f4e9216895f5",
"version_major": 2,
"version_minor": 0
},
@@ -100,7 +100,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "2216025f69ba44daa1d01f96a907fff0",
+ "model_id": "cd1e6b69d8c64b27b54e8623f4d08b70",
"version_major": 2,
"version_minor": 0
},
@@ -126,12 +126,12 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "9064d96ce5344a8793140b64d91e1312",
+ "model_id": "3a116fcf137a4c8fb667bbfe83db4ffe",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
- "ToggleButton(value=True, description='Virtual stage')"
+ "ToggleButton(value=False, description='Virtual stage')"
]
},
"metadata": {},
@@ -218,7 +218,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "32759c64f20f4d469d57b12a17d4a3cf",
+ "model_id": "f3556e2d23ce4f0aa7d7ab4c44494144",
"version_major": 2,
"version_minor": 0
},
@@ -232,7 +232,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "d60017a2c2a34b7cac0ad1322768790b",
+ "model_id": "b6214ad935aa47f79aba7d57995b65be",
"version_major": 2,
"version_minor": 0
},