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notebooks/experimental_xray_data/08_data_from_soleil_swing.ipynb

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"id": "b9fdba5b-a01b-4849-b3ce-79d938be2525",
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"metadata": {},
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"## The data - inspection via tree search\n",
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"## Data inspection via tree search\n",
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"| **Data file** | **Type** | **Download** | **Courtesy of** | **Reference** |\n",
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"| :- | :- | :- | :-: | :-: |\n",
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"id": "16cd9690-0421-4100-a515-bae74c61bd55",
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"## The data - finding the required bits of information\n",
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"## Finding the required bits of information\n",
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"In order to attempt a successful reconstruction, we need \n",
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"id": "f7e6f988-bded-49f7-b702-84b2ccb4a5e4",
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"metadata": {},
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"## The data - loading into memory and inspecting metadata\n",
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"## Loading data into memory and inspecting metadata\n",
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"It is now time to look at the data a bit more closely. First, we load everything into memory and print out some overall information:\n",
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"id": "faa67011-68bd-4e64-a9b2-91b04558cace",
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"## The data - plotting scan positions\n",
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"## Plotting the scan positions\n",
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"Let's look at the actual data starting with the scan positions. First we plot the two position arrays (```posx``` and ```posz```) against each other\n",
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"id": "4eee548f-d0b3-4325-8c73-b3a0ba6c6952",
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"metadata": {},
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"## The data - Plotting the diffraction patterns\n",
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"## Plotting the diffraction patterns\n",
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"Next, we look at the diffraction data. Plotting the first image\n",
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"id": "7ac12a21-faad-41f3-8f82-9fa26a4bb89e",
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"metadata": {},
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"## The data - creating and saving a mask of invalid pixels\n",
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"## Creating and saving a mask of invalid pixels\n",
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"To determine a mask of invalid pixels, it seems like we can simply threshold the first diffraction pattern\n",
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"id": "33039870-aed2-4941-b573-e11db1c6f5de",
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"## The reconstruction - initial steps\n",
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"## Initial reconstruction steps\n",
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"There are other tutorials that already explain the different sections of the parameter tree, but it might be worth to go through them once again.\n",
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"After an initial part with imports\n",
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"id": "1054f3aa-ac5e-49b5-b892-7599f1c62ccf",
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"metadata": {},
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"## The reconstruction - optimising the initial probe\n",
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"## Optimising the initial probe\n",
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"In order to inspect the initial probe calculated by PtyPy, the easiest way is to take the first pod and look at ```pod.probe```. We can also us the forward projector ```pod.fw()``` to calculate how our initial probe looks like in Fourier space and compare it to the diffraction data\n",
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"id": "7acdc8e7-b003-48cb-8b2d-c61f9d442b7f",
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"metadata": {},
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"## The reconstruction - let's give it a go\n",
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"## Let's give the reconstruction a go\n",
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"We can largerly use the same parameter as outlined above, with a few changes. First, we need to load the cupy engines\n",
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"id": "ee229b68-fb1e-442d-bfc5-bbaa26520ad0",
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"metadata": {},
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"## Run the reconstruction - let's make it work\n",
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"## Let's make it work\n",
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"We have now arrived at arguably the most difficult part of our task to reconstruct new data from scratch. We think that we have provided all the correct data or at least some reasonable estimates, but the reconstruction still looks completely wrong. At this point, it is advised to carefully check that all the provided numbers have the correct units, i.e. photon energy, detector distance, detector pixel size, the scan positions and they are indeed correct. If we are using a mask, we should also double check that it is loaded correctly or if it needs to be inverted. Once we have double checked all of this, there is one last barrier to overcome: choosing the correct coordinate system. \n",
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