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clean up notebook
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‎FAIRFlow_Notebook.ipynb‎

Lines changed: 24 additions & 142 deletions
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "6011110445794fc8a2056721b1a92751",
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"model_id": "415784f14e8e4f7d89075c2ce35a427f",
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"version_major": 2,
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"version_minor": 0
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},
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": 5,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "52abbeb906044c99b1546ae9094e12ac",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"FileChooser(path='/home/shambles/FAIRFlow', filename='', title='Select the dataset file', show_hidden=False, s…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"%reload_ext autoreload\n",
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"%autoreload 2\n",
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"from ipyfilechooser import FileChooser\n",
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"from pathlib import Path\n",
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"root = Path.cwd()\n",
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"fc = FileChooser(root)\n",
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"fc.title = 'Select the dataset file'\n",
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"display(fc)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "28a398e19f5747fd86f2c2751737d367",
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"model_id": "82696aadda634598ad82eac6f4e9438f",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Dropdown(description='Choose prechannel', layout=Layout(width='100%'), options=(), value=None)"
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"VBox(children=(HBox(children=(Dropdown(description='Choose dataset', layout=Layout(width='auto'), options=((''…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"from ipywidgets import widgets\n",
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"widget_choose_prechannel = widgets.Dropdown(\n",
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" description = 'Choose prechannel',\n",
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" # full_layout = widgets.Layout(width='auto')\n",
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" layout = widgets.Layout(width='100%')\n",
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")\n",
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"display(widget_choose_prechannel)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 69,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"PosixPath('/home/shambles/FAIRFlow')"
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]
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},
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"execution_count": 69,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"Path.cwd()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [
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{
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"ename": "NameError",
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"evalue": "name 'Measurement' is not defined",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
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"Cell \u001b[0;32mIn[1], line 13\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[38;5;66;03m# Import tools for data processing, analysis, and DaRUS upload\u001b[39;00m\n\u001b[1;32m 12\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mFAIRDaRUS\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mtools\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m DaRUS_upload\n\u001b[0;32m---> 13\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mFAIRFlow\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mtools\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mlogger_setup\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m setup_logger\n\u001b[1;32m 14\u001b[0m \u001b[38;5;66;03m# from FAIRFlow.tools import initialize_dataset, reading_raw_data_widget_new, analyzing_raw_data_widget\u001b[39;00m\n\u001b[1;32m 15\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mFAIRFlow\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mtools\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m initialize_dataset, reading_raw_data_widget, analyzing_raw_data_widget\n",
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"File \u001b[0;32m~/FAIRFlow/FAIRFlow/tools/__init__.py:1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01minitialize\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m initialize_dataset\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01macquisition\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m reading_raw_data_widget\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mnew_acquisition\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m reading_raw_data_widget_new\n",
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"File \u001b[0;32m~/FAIRFlow/FAIRFlow/tools/initialize.py:8\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mIPython\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mdisplay\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m display, clear_output\n\u001b[1;32m 7\u001b[0m \u001b[38;5;66;03m# Import Dataset\u001b[39;00m\n\u001b[0;32m----> 8\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mFAIRFlow\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcore\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Dataset\n\u001b[1;32m 11\u001b[0m \u001b[38;5;28;01mclass\u001b[39;00m \u001b[38;5;21;01minitialize_dataset\u001b[39;00m:\n\u001b[1;32m 13\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_save_dataset\u001b[39m(\u001b[38;5;28mself\u001b[39m,_):\n",
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"File \u001b[0;32m~/FAIRFlow/FAIRFlow/core/__init__.py:1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mdataset\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Dataset\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mexperiment\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Experiment\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mplantsetup\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m PlantSetup\n",
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"File \u001b[0;32m~/FAIRFlow/FAIRFlow/core/dataset.py:12\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01msdRDM\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mtools\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mutils\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m elem2dict\n\u001b[1;32m 11\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mplantsetup\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m PlantSetup\n\u001b[0;32m---> 12\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmeasurement\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Measurement\n\u001b[1;32m 13\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspeciesdata\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m SpeciesData\n\u001b[1;32m 14\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mexperiment\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Experiment\n",
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"File \u001b[0;32m~/FAIRFlow/FAIRFlow/core/measurement.py:22\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmetadata\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Metadata\n\u001b[1;32m 18\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcomponent\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Component\n\u001b[1;32m 21\u001b[0m \u001b[38;5;129;43m@forge_signature\u001b[39;49m\n\u001b[0;32m---> 22\u001b[0m \u001b[38;5;28;43;01mclass\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;21;43;01mMeasurement\u001b[39;49;00m\u001b[43m(\u001b[49m\u001b[43msdRDM\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mDataModel\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msearch_mode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43munordered\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m:\u001b[49m\n\u001b[1;32m 23\u001b[0m \u001b[38;5;250;43m \u001b[39;49m\u001b[38;5;124;43;03m\"\"\"\"\"\"\u001b[39;49;00m\n\u001b[1;32m 25\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mid\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mOptional\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;28;43mstr\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mattr\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 26\u001b[0m \u001b[43m \u001b[49m\u001b[43mname\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mid\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 27\u001b[0m \u001b[43m \u001b[49m\u001b[43mdescription\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mUnique identifier of the given object.\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 28\u001b[0m \u001b[43m \u001b[49m\u001b[43mdefault_factory\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mlambda\u001b[39;49;00m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mstr\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43muuid4\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 29\u001b[0m \u001b[43m \u001b[49m\u001b[43mxml\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m@id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 30\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n",
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"File \u001b[0;32m~/FAIRFlow/FAIRFlow/core/measurement.py:171\u001b[0m, in \u001b[0;36mMeasurement\u001b[0;34m()\u001b[0m\n\u001b[1;32m 160\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mexperimental_data\u001b[38;5;241m.\u001b[39mappend(Data(\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mparams))\n\u001b[1;32m 161\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mexperimental_data[\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m]\n\u001b[1;32m 163\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21madd_measurement_to_experimental_data\u001b[39m(\n\u001b[1;32m 164\u001b[0m \u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m 165\u001b[0m measurement_type: Optional[MeasurementType] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 166\u001b[0m metadata: List[Metadata] \u001b[38;5;241m=\u001b[39m ListPlus(),\n\u001b[1;32m 167\u001b[0m experimental_data: List[Union[Data, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mMeasurement\u001b[39m\u001b[38;5;124m\"\u001b[39m]] \u001b[38;5;241m=\u001b[39m ListPlus(),\n\u001b[1;32m 168\u001b[0m source: Optional[Component] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 169\u001b[0m \u001b[38;5;28mid\u001b[39m: Optional[\u001b[38;5;28mstr\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 170\u001b[0m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[0;32m--> 171\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[43mMeasurement\u001b[49m:\n\u001b[1;32m 172\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 173\u001b[0m \u001b[38;5;124;03m This method adds an object of type 'Measurement' to attribute experimental_data\u001b[39;00m\n\u001b[1;32m 174\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 180\u001b[0m \u001b[38;5;124;03m source (): measuring device the data stems from.. Defaults to None\u001b[39;00m\n\u001b[1;32m 181\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[1;32m 182\u001b[0m params \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m 183\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmeasurement_type\u001b[39m\u001b[38;5;124m\"\u001b[39m: measurement_type,\n\u001b[1;32m 184\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmetadata\u001b[39m\u001b[38;5;124m\"\u001b[39m: metadata,\n\u001b[1;32m 185\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mexperimental_data\u001b[39m\u001b[38;5;124m\"\u001b[39m: experimental_data,\n\u001b[1;32m 186\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msource\u001b[39m\u001b[38;5;124m\"\u001b[39m: source,\n\u001b[1;32m 187\u001b[0m }\n",
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"\u001b[0;31mNameError\u001b[0m: name 'Measurement' is not defined"
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]
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}
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],
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"source": [
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"# Activate autoreload to keep on track with changing modules\n",
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"%reload_ext autoreload\n",
@@ -276,7 +192,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 17,
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"execution_count": 9,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -339,52 +255,6 @@
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"rrdw.species_file.value = str(root)+'/data/faraday_efficiency/additional_data/species_data.yaml'"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"# rrdw._scenario_selective_oxidation.\n",
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"rrdw.widget_file_chooser.default_path = \"/home/shambles/FAIRFlow/data/selective_oxidation/raw_data/GC/tl110511_µ-Reaktor_beschichtet_5vol%_350°C/\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
355-
"metadata": {},
356-
"outputs": [],
357-
"source": [
358-
"import pandas as pd\n",
359-
"pd.set_option('display.max_colwidth', None)\n",
360-
"#strip the path from whitespace\n",
361-
"# stripp\n",
362-
"paths = rrdw.mydata_df['Filename'].apply(lambda x: PureWindowsPath(x).name)\n",
363-
"# apply(lambda x: x.strip('/s'))\n",
364-
"print(paths)\n",
365-
"# print(paths.apply(lambda x: x.name).astype(str))"
366-
]
367-
},
368-
{
369-
"cell_type": "code",
370-
"execution_count": 45,
371-
"metadata": {},
372-
"outputs": [
373-
{
374-
"name": "stdout",
375-
"output_type": "stream",
376-
"text": [
377-
"tl110419_5vol%_350°c_a10k_vg21_µ-reaktor_beschichtet_001-rep1.dat\n"
378-
]
379-
}
380-
],
381-
"source": [
382-
"path = PureWindowsPath(r'c:\\ezchrom elite\\enterprise\\projects\\default\\data\\tl110419_5vol%_350°c_a10k_vg21_µ-reaktor_beschichtet_001-rep1.dat')\n",
383-
"# path = PureWindowsPath(r'\\hure\\pisse\\kacke\\test.txt')\n",
384-
"# path = Path('hure/pisse/kacke/test.txt')\n",
385-
"print(path.name)"
386-
]
387-
},
388258
{
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"cell_type": "markdown",
390260
"metadata": {},
@@ -397,13 +267,13 @@
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},
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{
399269
"cell_type": "code",
400-
"execution_count": null,
270+
"execution_count": 12,
401271
"metadata": {},
402272
"outputs": [
403273
{
404274
"data": {
405275
"application/vnd.jupyter.widget-view+json": {
406-
"model_id": "f812ea94bba14d598f2859f335e52322",
276+
"model_id": "d60cbd8c90ce466eaa019e923f05a958",
407277
"version_major": 2,
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"version_minor": 0
409279
},
@@ -414,10 +284,22 @@
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"metadata": {},
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"output_type": "display_data"
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},
287+
{
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"name": "stderr",
289+
"output_type": "stream",
290+
"text": [
291+
"\n",
292+
"GC measurement already contains an assignment. Use this assignment rather than the default dictionary.\n",
293+
"\n",
294+
"\n",
295+
"GC measurement already contains an assignment. Use this assignment rather than the default dictionary.\n",
296+
"\n"
297+
]
298+
},
417299
{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
420-
"model_id": "e82ca24d09a044e2b9898f9f5f759d7b",
302+
"model_id": "e492d47d660145d9aede655bcdbf17c1",
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"version_major": 2,
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"version_minor": 0
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},
@@ -431,7 +313,7 @@
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
434-
"model_id": "f1738cb445bb49eaa3155bc6d5f63f51",
316+
"model_id": "3f6082011c6f47eea2ed154381edfa9c",
435317
"version_major": 2,
436318
"version_minor": 0
437319
},

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