We Keep Coding

Is it possible to turn a low quality image into a high quality one with Python?

I made a tif image based on a 3d model of a woodsheet. (x, y, z) represents a point in a 3d space. I simply map (x, y) to a pixel position in the image and (z) to the greyscale value of that pixel. It worked as I have imagined. Then I ran into a low-resolution problem when I tried to print it. The tif image would get pixilated badly as soon as it zooms out. My research suggests that I need to increase the resolution of the image. So I tried a few super-resolution algos found from online sources, including this one https://learnopencv.com/super-resolution-in-opencv/
The final image did get a lot bigger in resolution (10+ times larger in either dimension) but the same problem persists - it gets pixilated as soon as it zooms out, just about the same as the original image.
Looks like quality of an image has something to do not only with resolution of it but also something else. When I say quality of image, I mean how clear the wood texture is in the image. And when I enlarge it, how sharp/clear the texture remains in the image. Can anyone shed some light on this? Thank you.
original tif
The algo generated tif is too large to be included here (32M)
Gigapixel enhanced tif
Update - Here is a recently achieved result: with a GAN-based solution
It has restored/invented some of the wood grain details. But the models need to be retrained.

In short, it is possible to do this via deep learning reconstruction like the Super Resolution package you referred to, but you should understand what something like this is trying to do and whether it is fit for purpose.
Generic algorithms like the Super Resolution is trained on variety of images to "guess" at details that is not present in the original image, typically using generative training methods like using the low vs high resolution version of the same image as training data.
Using a contrived example, let's say you are trying to up-res a picture of someone's face (CSI Zoom-and-Enhance style!). From the algorithm's perspective, if a black circle is always present inside a white blob of a certain shape (i.e. a pupil in an eye), then next time it the algorithm sees the same shape it will guess that there should be a black circle and fill in a black pupil. However, this does not mean that there is details in the original photo that suggests a black pupil.
In your case, you are trying to do a very specific type of up-resing, and algorithms trained on generic data will probably not be good for this type of work. It will be trying to "guess" what detail should be entered, but based on a very generic and diverse set of source data.
If this is a long-term project, you should look to train your algorithm on your specific use-case, which will definitely yield much better results. Otherwise, simple algorithms like smoothing will help make your image less "blocky", but it will not be able to "guess" details that aren't present.

Converting GeoJSON to a raster image using rasterio

I am hoping for advice as to how I can convert GeoJSON geometry into a tif image using rasterio. I have tried a lot of things, but all of them do not rasterize all the shapes found in the GeoJSON (more like 80% of the file is rasterized). How can I ensure all the geometry is rasterized and is of adequate size? Let me know if my question is unclear.

Your problem stems from the fact that when you rasterize a shape, using gdal_translate for example, you must determine the resolution of the raster, and it must be chosen in accordance to the "size" of your feature vectors if you want your raster to retain enough information.
If you do not want to lose too many details in the rasterization process, I guess a good rule of thumb would be to set the resolution to be lower than the typical size of your individual features. For example, if your features look like squares ~1km large, a "good" resolution would be in the 10-100m range.
A way to programmatically get the typical size of your features would be to compute their minimum_rotated_rectangle for example: https://shapely.readthedocs.io/en/stable/manual.html#object.minimum_rotated_rectangle

Automatically find optimal image threshold value from density of histogram plot

I'm looking to perform optical character recognition (OCR) on a display, and want the program to work under different light conditions. To do this, I need to process and threshold the image such that there is no noise surrounding each digit, allowing me to detect the contour of the digit and perform OCR from there. I need the threshold value I use to be adaptable to these different light conditions. I've tried adaptive thresholding, but I haven't been able to get it to work.
My image processing is simple: load the image (i), grayscale i (g), apply a histogram equalization to g (h), and apply a binary threshold to h with a threshold value = t. I've worked with a couple of different datasets, and found that the optimal threshold value to make the OCR work consistently lies within the range of highest density in a histogram plot of (h) (the only part of the plot without gaps).
A histogram of (h). The values t=[190,220] are optimal for OCR. A more complete set of images describing my problem is available here: http://imgur.com/a/wRgi7
My current solution, which works but is clunky and slow, checks for:
1. There must be 3 digits
2. The first digit must be reasonably small in size
3. There must be at least one contour recognized as a digit
4. The digit must be recognized in the digit dictionary
Barring all cases being accepted, the threshold is increased by 10 (beginning at a low value) and an attempt is made again.
The fact that I can recognize the optimal threshold value on the histogram plot of (h) may just be confirmation bias, but I'd like to know if there's a way I can extract the value. This is different from how I've worked with histograms before, which has been more on finding peaks/valleys.
I'm using cv2 for image processing and matplotlib.pyplot for the histogram plots.

Check this: link it really not depend on density, it works because you did separation of 2 maximums. Local maximums are main classes foreground - left local maximum (text pixels), and background right local maximum (white paper). Optimal threshold should optimally separate these maximums. And the optimal threshold value lies in local minimum region between two local maximums.

At first, I thought "well, just make a histogram of the indexes in which data appears" which would totally work, but I don't think that will actually solve your underlying work you want to do.
I think you're misinterpreting histogram equalization. What histogram equalization does is thins out the histogram in highly concentrated areas so that if you take different bin sizes with the histogram, you'll get more or less equal quantity inside the bins. The only reason those values are dense is specifically because they appear less in the image. Histogram equalization makes other, more popular values, appear less. And the reason that range works out well is, as you see in the original grayscale histogram, values between 190 and 220 are really close to where the image begins to get bright again; i.e., where there is a clear demarkation of bright values.
You can see the way equalizeHist works directly by plotting histograms with different bin sizes. For example, here's looping over bin sizes from 3 to 20:
Edit: So just to be clear, what you want is this demarked area between the lower bump and the higher bump in your original histogram. You don't need to use equalized histograms for this. In fact, this is what Otsu thresholding (following Otsu's method) actually does: you assume the data follows a bimodal distribution, and find the point which clearly marks the point between the two distributions.

Basically, what you're asking is to find the indexes of the longest sequence of non-zero element in a 256 x 1 array.
Based on this answer, you should get what you want like this :
import cv2
import numpy as np
# load in grayscale
img = cv2.imread("image.png",0)
hist = cv2.calcHist([img],[0],None,[256],[0,256])
non_zero_sequences = np.where(np.diff(np.hstack(([False],hist!=0,[False]))))[0].reshape(-1,2)
longest_sequence_id = np.diff(non_zero_sequences,axis=1).argmax()
longest_sequence_start = non_zero_sequences[longest_sequence_id,0]
longest_sequence_stop = non_zero_sequences[longest_sequence_id,1]
Note that it is untested.

I would also recommend to use an automatic thresholding method like the Otsu's method (here a nice explanation of the method).
In Python OpenCV, you have this tutorial that explains how to do Otsu's binarization.
If you want to experiment other automatic thresholding methods, you can look at the ImageJ / Fiji software. For instance, this page summarizes all the methods implemented.
Grayscale image:
Results:
If you want to reimplement the methods, you can check the source code of the Auto_Threshold plugin. I used Fiji for this demo.

calculate particle size distribution from AFM measurements

I am trying to obtain a radius and diameter distribution from some AFM (Atomic force microscopy) measurements. So far I am trying out Gwyddion, ImageJ and different workflows in Matlab.
At the moment the best results I have found is to use Gwyddion and to take the Phase image, high pass filter it and then try an edge detection with 'Laplacian of Gaussian'. The result is shown in figure 3. However this image is still too noisy and doesnt really capture the edges of all the particles. (some are merged together others do not have a clear perimeter).
In the end I need an image which segments each of the spherical particles which I can use for blob detection/analysis to obtain size/radius information.
Can anyone recommend a different method?
[

I would definitely try a Granulometry, it was designed for something really similar. There is a good explanation of granulometry here starting page 158.
The granulometry will perform consecutive / increasing openings that will erase the different patterns according to their dimensions. The bigger the pattern, the latter it will be erased. It will give you a curve that represent the pattern dimension distributions in your image, so exactly what you want.
However, it will not give you any information about the position inside the image. If you want to have a rough modeling of the blobs present in your image, you can take a look to the Ultimate Opening.

Maybe you can use Avizo, it's a powerful software for dealing with image issues, especially for three D data (CT)

Converting an AutoCAD model to a matrix of points/volumes with the mass density specified at each location

I am an experimental physicist (grad student) that is trying to take an AutoCAD model of the experiment I've built and find the gravitational potential from the whole instrument over a specified volume. Before I find the potential, I'm trying to make a map of the mass density at each point in the model.
What's important is that I already have a model and in the end I'll have a something that says "At (x,y,z) the value is d". If that's an crazy csv file, a numpy array, an excel sheet, or... whatever, I'll be happy.
Here's what I've come up with so far:
Step 1: I color code the AutoCAD file so that color associates with material.
Step 2: I send the new drawing/model to a slicer (made for 3D printing). This takes my 3D object and turns it into equally spaced (in z-direction) 2d objects... but then that's all output as g-code. But hey! G-code is a way of telling a motor how to move.
Step 3: This is the 'hard part' and the meat of this question. I'm thinking that I take that g-code, which is in essence just a set of instructions on how to move a nozzle and use it to populate a numpy array. Basically I have 3D array, each level corresponds to one position in z, and the grid left is my x-y plane. It reads what color is being put where, and follows the nozzle and puts that mass into those spots. It knows the mass because of the color. It follows the path by parsing the g-code.
When it is done with that level, it moves to the next grid and repeats.
Does this sound insane? Better yet, does it sound plausible? Or maybe someone has a smarter way of thinking about this.
Even if you just read all that, thank you. Seriously.

Does this sound insane? Better yet, does it sound plausible?
It's very reasonable and plausible. Using the g-code could do that, but it would require a g-code interpreter that could map the instructions to a 2D path. (Not 3D, since you mentioned that you're taking fixed z-slices.) That could be problematic, but, if you found one, it could work, but may require some parser manipulation. There are several of these in a variety of languages, that could be useful.
SUGGESTION
From what you describe, it's akin to doing a MRI scan of the object, and trying to determine its constituent mass profile along a given axis. In this case, and unlike MRI, you have multiple colors, so that can be used to your advantage in region selection / identification.
Even if you used a g-code interpreter, it would reproduce an image whose area you'll still have to calculate, so noting that and given that you seek to determine and classify material composition by path (in that the path defines the boundary of a particular material, which has a unique color), there may be a couple ways to approach this without resorting to g-code:
1) If the colors of your material are easily (or reasonably) distinguishable, you can create a color mask which will quantify the occupied area, from which you can then determine the mass.
That is, if you take a photograph of the slice, load the image into a numpy array, and then search for a specific value (say red), you can identify the area of the region. Then, you apply a mask on your array. Once done, you count the occupied elements within your array, and then you divide it by the array size (i.e. rows by columns), which would give you the relative area occupied. Since you know the mass of the material, and there is a constant z-thickness, this will give you the relative mass. An example of color masking using numpy alone is shown here: http://scikit-image.org/docs/dev/user_guide/numpy_images.html
As such, let's define an example that's analogous to your problem - let's say we have a picture of a red cabbage, and we want to know which how much of the picture contains red / purple-like pixels.
To simplify our life, we'll set any pixel above a certain threshold to white (RGB: 255,255,255), and then count how many non-white pixels there are:
from copy import deepcopy
import numpy as np
import matplotlib.pyplot as plt
def plot_image(fname, color=128, replacement=(255, 255, 255), plot=False):
# 128 is a reasonable guess since most of the pixels in the image that have the
# purplish hue, have RGB's above this value.
data = imread(fname)
image_data = deepcopy(data) # copy the original data (for later use if need be)
mask = image_data[:, :, 0] < color # apply the color mask over the image data
image_data[mask] = np.array(replacement) # replace the match
if plot:
plt.imshow(image_data)
plt.show()
return data, image_data
data, image_data = plot_image('cabbage.jpg') # load the image, and apply the mask
# Find the locations of all the pixels that are non-white (i.e. 255)
# This returns 3 arrays of the same size)
indices = np.where(image_data != 255)
# Now, calculate the area: in this case, ~ 62.04 %
effective_area = indices[0].size / float(data.size)
The selected region in question is shown here below:
Note that image_data contains the pixel information that has been masked, and would provide the coordinates (albeit in pixel space) of where each occupied (i.e. non-white) pixel occurs. The issue with this of course is that these are pixel coordinates and not a physical one. But, since you know the physical dimensions, extrapolating those quantities are easily done.
Furthermore, with the effective area known, and knowledge of the physical dimension, you have a good estimate of the real area occupied. To obtain better results, tweak the value of the color threshold (i.e. color). In your real-life example, since you know the color, search within a pixel range around that value (to offset noise and lighting issues).
The above method is a bit crude - but effective - and, it may be worth exploring using it in tandem with edge-detection, as that could help improve the region identification, and area selection. (Note that isn't always strictly true!) Also, color deconvolution may be useful: http://scikit-image.org/docs/dev/auto_examples/color_exposure/plot_ihc_color_separation.html#sphx-glr-auto-examples-color-exposure-plot-ihc-color-separation-py
The downside to this is that the analysis requires a high quality image, good lighting; and, most importantly, it's likely that you'll lose some of the more finer details of the edges, which would impact your masses.
2) Instead of resorting to camera work, and given that you have the AutoCAD model, you can use that and the software itself in addition to the above prescribed method.
Since you've colored each material in the model differently, you can use AutoCAD's slicing tool, and can do something similar to what the first method suggests doing physically: slicing the model, and taking pictures of the slice to expose the surface. Then, using a similar method described above of color masking / edge detection / region determination through color selection, you should obtain a much better and (arguably) very accurate result.
The downside to this, is that you're also limited by the image quality used. But, as it's software, that shouldn't be much of an issue, and you can get extremely high accuracy - close to its actual result.
The last suggestion to improve these results would be to script numerous random thin slicing of the AutoCAD model along a particular directional vector shared by every subsequent slice, exporting each exposed surface, analyzing each image in the manner described above, and then collecting those results to given you a Monte Carlo-like and statistically quantifiable determination of the mass (to correct for geometry effects due to slicing along one given axis).