QGrain

An open-source and easy-to-use software for the comprehensive analysis of grain-size distributions

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Advanced installation

Note: this way of installation is for the user who has experience in Python and Shell (i.e. command-line interface) or is willing to take the time to learn them.

The QGrain software is a Python module. So, if you have experience with Python, you can install it from PyPI. This way of installation is more flexible because the source codes can be modified easily. If there is a low-level bug, you can modify the codes to timely fix it by yourself, no need to wait for the author of QGrain to fix it and publish the new version. In addition, you can write codes to use QGrain for some special application scenarios. For example, load the fitting results and customize the plots. Python and the third-party modules used in QGrain are all cross-platform, this means QGrain also is cross-platform, theoretically. However, some dependent modules (e.g., PyTorch) may not have a binary distribution for some unpopular operating systems, you may need to solve this dependency problem by compiling these modules from sources. Don’t worry, it’s not a problem for most operating systems.

Install the Python

For Linux and Mac OS X users, a relatively old version of Python is built-in. Windows users need to install it from the official website.

You can run the command python or python3 in your Terminal to check if Python is existing.

Note: Using python or python3 depends on the alias or the filename of your Python3 interpreter, rather than you can choose Python2 or Python3 at liberty. Python2 is too old and has been obsoleted. For Unix-like operating systems, python3 usually is correct, and for Windows, python usually is correct.

If you have Python3 installed on your computer, you can see the text which is similar to below. You can see the version of your Python. And the >>> symbols hint that you have entered the interactive model of Python’s interpreter. Type quit() to quit this model and back to the terminal.

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username:~$ python3
Python 3.8.5 (default, Jan 27 2021, 15:41:15)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>

If there is no Python, just follow the guide in the official website of Python to install it.

Install QGrain

We have uploaded QGrain to PyPI. You can install it by running pip or pip3 in the Terminal.

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pip3 install QGrain

For the users in China, using the mirror provided by Tsinghua University may be faster.

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pip3 install -i https://pypi.tuna.tsinghua.edu.cn/simple QGrain

Run pip3 install -U QGrain to check and update QGrain.

If you do not have the pip, just use the package management tool to install it.

For example, the command for Ubuntu is:

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sudo apt update
sudo apt install python3-pip

In addition, you can download the codes from our GitHub repository.

You can clone the repository by running the following command if you have git installed.

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git clone https://github.com/yuriok/QGrain.git

Then, you will see similar information below.

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username:~$ git clone https://github.com/yuriok/QGrain.git
Cloning into 'QGrain'...
remote: Enumerating objects: 2792, done.
remote: Counting objects: 100% (1526/1526), done.
remote: Compressing objects: 100% (742/742), done.
remote: Total 2792 (delta 1042), reused 1244 (delta 781), pack-reused 1266
Receiving objects: 100% (2792/2792), 2.02 MiB | 24.00 KiB/s, done.
Resolving deltas: 100% (1871/1871), done.

When it finished, the source codes have been downloaded into the QGrain folder of the working directory. Change the working directory to QGrain, and use pip to install it.

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cd QGrain
pip3 install .

Or, you can download the pure codes directly by clicking here. If you choose to download the zip file, please extract it. Then, you should change the directory to the extracted folder, and run the command pip3 install ..

Try QGrain

Now, everything is ok. You can run python3 -m QGrain command in your terminal to start the GUI of QGrain.

If it goes well, you can see the interface below.

The screenshot of the initial interface

Also, you can use QGrain as a Python module, import it in your Python codes and use the class and function provided by QGrain. For example, you can calculate the statistic parameters using the following codes. Note: the APIs of QGrain will be changed a lot, it’s not recommended to use this method for common requirements.

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# import the method to generate artificial samples
from QGrain.models.artificial import get_random_sample
# import the method to calculate the statistic parameters
from QGrain.statistic import get_all_statistic

# generate test sample
sample = get_random_sample()
# check the generating parameters
print(sample.parameter.fractions)
for comp in sample.parameter.components:
print(comp.moments)

# get the statistic parameters and classification groups
all_statistic = get_all_statistic(sample.classes_μm, sample.classes_φ, sample.distribution)
print(all_statistic)

You will see the statistic parameters and the classification groups like below:

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{'arithmetic': {'mean': 21.144515863718222, 'std': 25.084414158797554, 'skewness': 2.920857741744253, 'kurtosis': 18.730985063587315}, 'geometric': {'mean': 9.684134657536994, 'std': 4.428361711788003, 'skewness': -0.6767708384230607, 'kurtosis': 2.716874606082691, 'std_description': 'Very poorly sorted', 'skewness_description': 'Fine skewed', 'kurtosis_description': 'Mesokurtic', 'median': 12.810636058031518, 'mean_description': 'Medium Silt', 'mode': 22.44036908603928, 'modes': (0.8933671843019261, 22.44036908603928)}, 'logarithmic': {'mean': 6.6981337719919, 'std': 2.1467781514716644, 'skewness': 0.6656247900909836, 'kurtosis': 2.706878223445299, 'std_description': 'Very poorly sorted', 'skewness_description': 'Fine skewed', 'kurtosis_description': 'Mesokurtic', 'median': 6.2865140813873825, 'mean_description': 'Medium Silt', 'mode': 5.477759785030356, 'modes': (10.128459117872664, 5.477759785030356)}, 'geometric_FW57': {'mean': 9.095310169432295, 'std': 4.5648431593499135, 'skewness': -0.3327285931766691, 'kurtosis': 0.9931902091662234, 'std_description': 'Very poorly sorted', 'skewness_description': 'Very fine skewed', 'kurtosis_description': 'Mesokurtic', 'median': 12.810636058031518, 'mean_description': 'Medium Silt', 'mode': 22.44036908603928, 'modes': (0.8933671843019261, 22.44036908603928)}, 'logarithmic_FW57': {'mean': 6.780661446975351, 'std': 2.190565292385788, 'skewness': 0.33272859317666903, 'kurtosis': 0.9931902091662237, 'std_description': 'Very poorly sorted', 'skewness_description': 'Very fine skewed', 'kurtosis_description': 'Mesokurtic', 'median': 6.2865140813873825, 'mean_description': 'Medium Silt', 'mode': 5.477759785030356, 'modes': (10.128459117872664, 5.477759785030356)}, 'GSM_proportion': (0.0, 0.0681, 0.9327000000000001), 'SSC_proportion': (0.0681, 0.7625000000000002, 0.1702), 'BGSSC_proportion': (0.0, 0.0, 0.0681, 0.7625000000000002, 0.1702), 'proportion': {('', 'Megaclasts'): 0.0, ('Very large', 'Boulder'): 0.0, ('Large', 'Boulder'): 0.0, ('Medium', 'Boulder'): 0.0, ('Small', 'Boulder'): 0.0, ('Very small', 'Boulder'): 0.0, ('Very coarse', 'Gravel'): 0.0, ('Coarse', 'Gravel'): 0.0, ('Medium', 'Gravel'): 0.0, ('Fine', 'Gravel'): 0.0, ('Very fine', 'Gravel'): 0.0, ('Very coarse', 'Sand'): 0.0, ('Coarse', 'Sand'): 0.0, ('Medium', 'Sand'): 0.0005, ('Fine', 'Sand'): 0.0088, ('Very fine', 'Sand'): 0.0588, ('Very coarse', 'Silt'): 0.1722, ('Coarse', 'Silt'): 0.23059999999999997, ('Medium', 'Silt'): 0.17370000000000002, ('Fine', 'Silt'): 0.1119, ('Very fine', 'Silt'): 0.0741, ('Very coarse', 'Clay'): 0.0654, ('Coarse', 'Clay'): 0.0638, ('Medium', 'Clay'): 0.03320000000000001, ('Fine', 'Clay'): 0.0070999999999999995, ('Very fine', 'Clay'): 0.0007}, 'group_Folk54': 'Slit', '_group_BP12_symbols': ['(s)', '(c)', 'SI'], 'group_BP12_symbol': '(s)(c)SI', 'group_BP12': 'Slightly Sandy Slightly Clayey Silt'}

Enable CUDA

Some functions (e.g., EMMA) of QGrain could use CUDA to accelerate the computation. By default, QGrain will install the CPU version of PyTorch, because not all users have a high-performance NVIDA GPU, and CPU is faster to handle a small dataset. It needs more steps to enable the CUDA, not only install a CUDA version of PyTorch, CUDA Toolkit and CUDNN also should be installed. Follow the guides of PyTorch and NVIDA to install them. If all of them have been installed, the CUDA option in the device setting could be selected.