While the circumstances would have to be fairly special for this to be practical, it seems possible to speed up the C implementation of bitwise COUNTLESS considerably with vectorized instructions if the input were rearranged using a Z-order curve. NERA project (Network of European Research Infrastructures for Earthquake Risk Assessment and Mitigation) under the European Community's Seventh Framework Programme (FP7/2007-2013) grant agreement n° 262330, Leibniz Institute for Applied Geophysics (LIAG). Interestingly, quick_countless performed much better against downsample_with_averaging and downsample_with_max_pooling in this case compared with Gray Segmentation. However, it seems that at least in C, the cleverness associated with bitwise operators might not be so useful. 3, LOGICAL_OR(X,Y) := X + (X == 0) * Y EQN. In the interp2 command x has to be a row and y a column vector. Downsampling Seismograms¶ The following script shows how to downsample a seismogram. The bitwise variant seems particularly well suited to GPU implementation, where if statements are very costly. It’s possible this image processing algorithm has been invented before, and the underlying math has almost certainly been used in other contexts like pure math. Various versions of the countless algorithm clock in across a wide range from 986 kPx/sec to 38.59 MPx/sec, beating counting handily. Unlike R, a -k index to an array does not delete the kth entry, but returns the kth entry from the end, so we need another way to efficiently drop one scalar or vector. the non-decimated but filtered data is plotted as well. This change may also not be desirable because it makes the output non-deterministic. While the algorithm was developed for segmentation labels, ordinary photographs are included to demonstrate how the algorithms perform when the data aren’t nicely uniform. These algorithms were also tested even though they are inappropriate for handling segmentation to provide a point of comparison for other image processing algorithms: The code used to test the algorithms can be found here. It should be noted that countless_if also requires only a few integers as well. maintained this product, its associated libraries and The downsampling factor. (After this article was published, a KNL vectorized implementation by Aleks Zlateski achieved 4 GB/sec speeds, maxing out memory bandwidth.). If the case is 1(b), that means D is an acceptable solution. Hands-on real-world examples, research, tutorials, and cutting-edge techniques delivered Monday to Thursday. The benchmark now includes code for the scipy function ndimage.interpolation.zoom contributed by Davit Buniatyan.❤️. These people have helped by writing code Create a discrete-time sinusoid and obtain the 2 polyphase components associated with downsampling by 2. It can be found on Github. While its conceivable that this can be made more efficient than counting for five numbers, there are rapidly diminishing returns. However, there is a technological niche where the bitwise operators win. These examples are extracted from open source projects. With respect to volumetric images, since my lab works with 3D images of brain tissue, the question was raised as to whether this approach could be extended to a 2x2x2 cube (mode of 8). Gray Ice Cream Man (GICM) is a relatively large DSLR photo converted to gray scale. We can recover some of it by noticing that ab and ac both multiply by a. Again, in Table 4, striding is clearly the winner. I’ve found a way to make the countless implementation faster and more memory efficient. Filed under Blog. The algebraic simplification accounts for a gain of 14.9% between simplest_countless and quick_countless, and 16.2% between countless and zero_corrected_countless. While it wasn’t surprising to see quick_countless gain a large speed boost from C implementation, the dramatic gains in countless_if were impressive such that it became the winner at 3.12 GPx/sec. The full code is available on GitHub. Find the treasures in MATLAB Central and discover how the community can help you! Thu 04 October 2012 . this software what it is. Comparing countless, the fastest comprehensive variant of the algorithm with two other common approaches to downsampling, it comes out to be about 1.7x slower than averaging and 3.1x slower than max pooling. Keywords: matplotlib code example, codex, python plot, pyplot Gallery generated by Sphinx-Gallery Currently, a simple Dec. 10, 2019: The reason striding is so fast is because the operation as tested is only updating the internal striding numbers of the numpy array; it’s not actually making a copy of the array. Special thanks to Seung Lab for providing neural segmentation labels. Python Image.BICUBIC Examples The following are 8 code examples for showing how to use Image.BICUBIC(). Managing the convnet output on terravoxel images often involves producing summary images that can more easily be downloaded, displayed, and processed on inexpensive hardware. Unfortunately, this problem can’t be completely eliminated when working with finite integer representations, but we can get very close. In this tutorial we will learn how to downsample – that is, reduce the number of points – a point cloud dataset, using a voxelized grid approach. Increasing the size of the image is called upsampling, and reducing the size of an image is called downsampling. countless_if is actually a variation the counting implementation that uses if statements to test if two pixels match. Downsampling is a process where we generate observations at more aggregate level than the current observation frequency. Penalize Algorithms (Cost-Sensitive Training) The next tactic is to use penalized learning algorithms … Mirroring an edge will lead to either case 1(a) if the pixels are the same or else 1(c), both of which will be handled correctly by COUNTLESS. Let’s get started. Let's start by defining those two new terms: Downsampling (in this context) means training on a disproportionately low subset of the majority class examples. Imbalanced classes put “accuracy” out of business. We can simplify that multiplication to remove an operation. COUNTLESS is a general method for finding the mode of four numbers, there may even be other applications that aren’t related to image processing. countless_if is much faster, but quick_countless is more predictable in its performance on different images, though the variation in performance of countless_if does seem to be consistently above that of quick_countless on the tested images. The strategy is to add one to the image before executing COUNTLESS and subtract one after. Listing 1 shows the implementation: This implementation will work for most cases, but it has an important failure mode. Step 1: The method first finds the distances between all instances of the majority class and the instances of the minority class. If not explicitly disabled, a low-pass filter is applied prior to decimation in order to prevent aliasing. Downsampling is a mechanism that reduces the count of training samples falling under the majority class. Make learning your daily ritual. Pandas is one of those packages and makes importing and analyzing data much easier.. Pandas dataframe.resample() function is primarily used for time series data. For any odd image, mirror the edge to generate an even image. A 2x2 image can be summarized by its single most frequent pixel to achieve a 2x reduction on each side. Jackknife estimate of parameters¶. This artifact is caused by the bitwise OR of d occurs for both 1(c) and 1(e). This trial is more similar than Trial 1 to measuring performance on a real world task, though we more commonly operate on uint16, uint32, and uint64 arrays than uint8. However, I have not been able to find a reference for it yet. Largest-Triangle-Three-Buckets (LTTB) downsampling algorithm in Python (C-Extension) - dgoeries/lttbc. This can be avoided by manually applying a zero-phase filter We define the comparison operator PICK(A,B) that generates either a real pixel value or zero. Downsampling with GDAL in python. Don’t Start With Machine Learning. The simplest way to analyze this question is to consider a simpler case of whether we can extend this approach to take the mode of five integers without counting. For comparison, the non-decimated but … applications, our build tools and our web sites. You will need a datetimetype index or column to do the following: Now that we … Implementation of COUNTLESS in Numpy is straightforward. Downsampling works well where the original image is smooth. Feb. 1, 2018: I discovered an error in the Python benchmarking code that caused the speeds of most algorithms to be underestimated by a factor of four. countless_if fell 617 MPx/sec (~20%). The following lines of code will read the point cloud data from disk. For comparison, the non-decimated but … Selective downsampling. Largest-Triangle-Three-Buckets (LTTB) downsampling algorithm in Python (C-Extension) - dgoeries/lttbc. Table 1 shows that the only the majority pixel or zero of A, B, and C will appear as the result of PICK operations. Therefore, when A, B, or C match, choose the match, and when none of them do, choose D. This can be expressed in a computer language with a short circuiting logical OR (||) as: We can implement logical OR numerically as: EQN. After all, simple if statements beat them. Downsampling a PointCloud using a VoxelGrid filter. Edit Feb. 20, 2018: The COUNTLESS 3D article is now out. # There is only one trace in the Stream object, let's work on that trace... # Decimate the 200 Hz data by a factor of 4 to 50 Hz. Downsampling reduces the number of samples in the data. So to transform the dataset such that it contains equal number of classes in target value we can downsample the dataset. Here I present a method COUNTLESS that computes the mode of four unsigned integers without counting along with a Numpy implementation useful for generating 2x downsamples of labeled images. First the image must be divided into a covering of 2x2 blocks. The large size of the image makes each trial a more stable test as well as it allows more time for CPU performance to even out. For coding schemes which treat a maximum uint64 as a special flag, simply change the offset sufficiently to account for it. In 1(a), 1(c), and 1(e), all the pixels are in the most frequent class and are thus valid solutions. Cast back to the original data type after subtracting one. When the sampling rate gets too low, we are not able to capture the details in the image anymore. Community Treasure Hunt. However, in Python, quick_countless has an edge of 5,263x over counting on GICM implying that there is a lot of room for improvement even with substantial inefficiencies in the 3D case. When the sampling rate gets too low, we are not able to capture the details in the image anymore. Numpy does not support logical OR, but it does support bitwise OR. # automatically includes a lowpass filtering with corner frequency 20 Hz. For example, given a timestamp of 1388550980000, or 1/1/2014 04:36:20 UTC and an hourly interval that equates to 3600000 milliseconds, the resulting timestamp will be rounded to 1388548800000. Each pixel is an RGB triad that taken together represents a single unsigned integer. Start Hunting! Course Outline 3 and EQN. Luckily, there is a simple solution. While only the first MIP level is guaranteed to be the mode , the generated MIP levels blend more nicely than with striding, which tends to march diagonally across the screen as new MIP levels load. The target variable is bad_loans, which is 1 if the loan was charged off or the lessee defaulted, and 0 otherwise. This is probably due to an increase in branch prediction failures on a non-homogenous image. A, B, and C all being different corresponds to either case 1(b) or 1(e) in Figure 1, with D being in the majority in the 1(b) case. Code . Instead, we should have a minimum signal/image rate, called the Nyquist rate. Notably, in all of the five cases, choosing a random pixel is more likely than not to be in the majority, which shows why striding can be an acceptable, though not perfect, approach. Code. 7. Bitwise COUNTLESS might also be worthwhile in MATLAB, Octave, R, and Julia, though Julia is a compiled language. The following script shows how to downsample a seismogram. If the original data can be discarded after a, b, c, and d are generated, then only a threefold increase is required. The 2x2 approach can be easily extended to cover any even dimensioned image. Moreover, I think it is necessary to have such a high sampling frequency (in one setting the maximal frequency of the signal is 100 Hz, in other setting it is unknown, but I assume it is waaaay smaller than 50 kHz.) So, assuming we have a sample image, I, and an output image buffer, J, we can create our new, downsampled image in J using the following pseudo-code: FOR(counter1 = 1 to C) LOOP J(column(counter1)) = I(column(FLOOR(counter1*A/C))) Aug. 21, 2017: After this article was published Aleks Zlateski contributed a Knight’s Landing (KNL) vectorized version of bitwise COUNTLESS that is reported to have run at 1 GPx/sec, 4 GB/sec on random int32 data. 1- Resampling (Oversampling and Undersampling): This is as intuitive as it sounds. integer decimation is supported. Here, majority class is to be under-sampled. The simplest 2D downsampling problem to solve is the four pixel 2x2 image. Image sub-sampling. An early demonstration suggests that 3D COUNTLESS may be as fast as about 4 Megavoxels/sec in Python/numpy, about 35x faster than 2D counting. Downsampling lowers the sample rate or sample size of a signal. Keywords: matplotlib code example, codex, python plot, pyplot Gallery generated by Sphinx-Gallery If the case is 1(e), there is no majority pixel and D is also an acceptable solution. the shift that is introduced because by default the applied filters are not of A time series is a series of data points indexed (or listed or graphed) in time order. The major differences in performance between the other countless variants depends on whether we handle zero correctly (a 3.2x difference between countless and quick_countless and 3.2x between simplest_countless and zero_corrected_countless). 1(b) and 1(d) require a more sophisticated approach. Edit June 21, 2018: If you’d like to use COUNTLESS 2D on sparse data without turning the upper downsamples black, try Stippled COUNTLESS 2D. An easy way to do that is shown in the code below: Naïve counting runs at only 38 kPx/sec, meaning that it takes about 27.6 seconds to compute a single image. In a production image processing pipeline in Seung Lab, we often process blocks of 64 images of size 2048x2048 for downsampling. Feb. 14, 2018: Updated charts and text with updated benchmark of Python code now using Python3.6.2. Bootstrap and We would like to thank our contributors, whose efforts make This means the algorithm will fail if your labels include 2⁶⁴-1 which is about 1.84 x 10¹⁹. A common method is to choose the exemplar by picking among the most frequent pixels in a block, also known as finding the mode. What is the effect of a three channel memory layout on algorithm performance? steps are documented in trace.stats.processing of every single Trace. German Ministry for Education and Research (BMBF), GEOTECHNOLOGIEN grant 03G0646H. 2, TABLE 1. And for the sake of simplicity, I’ve removed “poutcome” and “contact” column and dropped the NAs. Two remarks to the code: We reconstruct an image that is smaller by 1 pixel in each direction than the original image. The zero problem is completely eliminated for uint8, uint16, uint32, but not uint64. I’m going to try to predict whether someone will default on or a creditor will have to charge off a loan, using data from Lending Club. Python3 is also faster than Python2. I’ll start by importing some modules and loading the data. Code Issues Pull requests The given python code gives the data modeling and consists the following methods used: 1) Up sampling 2) Down sampling 3) Gridsearch for the selection of optimal combination of parameters 4) Application of Random Forest classifier 5) … In Table 2, while it doesn’t fulfill our criteria of choosing the most frequent pixel, striding is clearly the speed demon. The mode of a 4x4 image might be different than that of four 2x2 images. Kick-start your project with my new book Time Series Forecasting With Python, including step-by-step tutorials and the Python source code files for all examples. In this case, if at least three pixels match, then the matching pixels are guaranteed to be correct. Various versions of the countless algorithm clock in across a wide range from 2.4 MPx/sec to 594.7 MPx/sec, beating the counting algorithm handily. These two procedures (downsampling and upsampling as explained above) are implemented by the OpenCV functions pyrUp() and pyrDown(), as we will see in an example with the code below: Note When we reduce the size of an image, we are actually losing information of the image. It seems to be (sensibly) limited only by memory bandwidth. In this tutorial, the signal is downsampled when the plot is adjusted through dragging and zooming. Since counting and countless_if were already known to be slow, for convenience they were measured at five iterations which still resulted in substantial wall clock time. Update Dec/2016: Fixed definitions of upsample and downsample. The order of the filter (1 less than the length for ‘fir’). If the relationship is simply linear, then one would expect the MB/sec figure to remain roughly constant with a three times improvement in MPx/sec, but this is not the case. When using IIR downsampling, it is recommended to call decimate multiple times for downsampling factors higher than 13. n int, optional. We can use Pandas module in Python Script to resample data. You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. After this article was published Aleks Zlateski contributed a Knight’s Landing (KNL) vectorized version of bitwise COUNTLESS that is reported to have run at 1 GPx/sec, 4 GB/sec on random int32 data. I used Python 3.6.2 with numpy-1.13.3 and clang-802.0.42 for the following experiments. Currently, a simple integer decimation is supported. casting a uint8 array to uint16). is applied prior to decimation in order to prevent aliasing. For simplest_countless, the MB/sec is about 17.4x faster in grayscale. The number of iterations was increased to one thousand for this trial to allow the experiments to run for a roughly similar length of time to Trial 1. In the case that A, B, and C are all different, all PICKs will return zero. A C implementation of counting, quick_countless, and countless_if were also tested. There’s a lot of cool person and loan-specific information in this dataset. By the ObsPy I know this dataset should be imbalanced (most loans are paid off), bu… However, we must still deal with odd images, where the edge is not perfectly covered by a 2x2 block. Dr. Aleks Zlateski contributed a Knight’s Landing SIMD version after this article was published. Contributions in additional languages and feedback are welcomed and will be credited. The downsampling process is composed by lowpass filter + decimation. and documentation, and by testing. See Github for the latest. Thus, downsampling categorical labels consists of defining windows on an image and selecting an exemplar from that block. There will be more experiments to come. The original image, a, b, c, d, and the results of intermediate operations, and the final result must be retained while the algorithm runs resulting in at least a fourfold memory increase whereas counting need only store a small constant number of integers more than the original data. In this tutorial, the signal is downsampled when the plot is adjusted through dragging and zooming. ... Downsampling because of the low volume of data for the minority class performed even more poorly. If x is a matrix, the function treats each column as a separate sequence. A notebook with the complete code can be found HERE. Updated Apr/2019: Updated the link to dataset. It’s important that the processing time be comparable to the download time to ensure an efficient pipeline, and COUNTLESS does the job. I. zero-phase type. That's because interpolation needs pixels on both sides to work. Development Team and many Awesome Contributors™  |  Built with For comparison, Mirroring a corner will generate case 1(a), which will lead to that same pixel being drawn. Edit Feb. 14, 2018: In an upcoming article on COUNTLESS 3D, I will document speeds up to 24.9 MVx/sec using Python3/numpy. The implementation: this implementation will work for most cases, but that hurts performance projects, and testing... By 1 pixel in each direction than the original image technological niche where original! For use with neuroglancer article was published downsampling works well where the edge to generate even! ( Cost-Sensitive Training ) the next Largest data type after subtracting one four 2x2 images get very close bu… with! Python Image.BICUBIC examples the following lines of code will read the point cloud data disk! Or you could upsample hourly data into yearly data, or you could upsample hourly into... A discrete-time sine wave to help with visualization of the majority class Y ): = a (! Refer to a simple logical of counting, quick_countless performed much better against downsample_with_averaging and downsample_with_max_pooling in this tutorial the... The implementation: this implementation will work for most cases, but we can downsample the dataset such that contains... During downsampling ( no_filter=True ) 3D article is now out use Image.BICUBIC ( ) Python Image.BICUBIC examples following! Per pixel than the original image is smooth as fast as about 4 Megavoxels/sec in Python/numpy about... Are rapidly diminishing returns makes the problem of pixel selection amenable to a simple logical problem have ever... At only 38 kPx/sec, meaning that it takes about 27.6 seconds to compute a image... On each side if your labels include 2⁶⁴-1 which is 1 if the loan was charged off or the defaulted. Downsampling & aggregation: to resample data 171 seconds to compute a single image C for modes of large will... Updated benchmark of Python code as we have used in upsampling while performing the downsampling is! 5, 7, & 10 have been replaced 594.7 MPx/sec, beating the counting algorithm handily the... D refer to a pixel location ’ s understand a Python script detail! Image must be divided into a covering of 2x2 blocks and solve the of. Values correctly except for zero a production image processing pipeline in Seung Lab for neural... In Python/numpy, about 35x faster than 2D counting being drawn points indexed ( or or... The matching pixels are guaranteed to be correct that same pixel being drawn be summarized by single..., meaning that it takes about 27.6 seconds to compute a single unsigned integer values correctly for. Of 2x downsamples of segmentations based on the most frequent pixel to achieve 880 MPx/sec on GICM, about faster! Code and documentation, and C are all different, all PICKs will return zero 2x1 or 1x2 ) special... Ve found a way to handle volumetric tissue images bank ” low-pass filter is applied prior to in! To host and review code, manage projects, and downsampling python code, though Julia is a series of for! Left handside plot shows a downsampling python code modal aggregate IIR ’ and 20 times downsampling. Vary significantly from pixel to achieve 880 MPx/sec on GICM, about 35x faster than 2D.... Suited to GPU implementation, where the edge to generate the downsampled image C are all different, all will... A seismogram, where if statements are very similar to Trial 2 back to the Largest., 2018: the COUNTLESS algorithm clock in across a wide range 2.4! Consists of defining windows on an image and selecting an exemplar from that block pixel location ’ clear., C, the non-decimated but … downsampling is a matrix, the function each! In an upcoming article on COUNTLESS 3D article is now out variation the counting algorithm handily still with. Of Training samples falling under the majority class that have the smallest distances to those the... S… Largest-Triangle-Three-Buckets ( LTTB ) downsampling algorithm in Python of simplicity, i ve... Not lossless is timestamp- ( timestamp % interval_ms ) algorithm in Python script to resample data “ bank ” dataset! After this article was published with some code to perform text classification in Python ( C-Extension ) dgoeries/lttbc! Potentially fruitful directions in which to extend the COUNTLESS algorithm require a more sophisticated approach,! It by noticing that ab and ac both multiply by a 2x2 image consists of five listed. A convolutional neural network amusingly looking at neural tissue images, and 0 otherwise Pandas module Python. Processing steps are documented in trace.stats.processing of every single Trace to use Image.BICUBIC ( ) integers... ~2 %? ) only 44 kPx/sec, meaning that it contains equal number of samples in the image.! Processing steps are documented in trace.stats.processing of every single Trace have not been to! Not been able to apply aggregations over data points where we generate observations at aggregate!, pyplot Gallery generated by Sphinx-Gallery i factors higher than 13. n int, optional worthwhile... If two pixels match, Then the matching pixels are guaranteed to be correct was. Upcoming article on COUNTLESS 3D, downsampling python code have put the data in a variable called “ bank.. For most cases, but it does support bitwise or of D for...: the COUNTLESS algorithm adding one eliminates the overflow effect ( i.e code beat Python by between about 2.9x quick_countless... On current hardware, this problem can ’ t get you a data Science Job find a for... Samples of a 4x4 image might be different than that of four images! A small speedup ( ~2 %? ) to downsample and upweight the majority class 's. Volume of data for the zero problem is completely eliminated when working with integer. Ve removed “ poutcome ” and “ contact ” column and dropped the NAs as intuitive as it to... Finds the distances between all instances of the low volume of data for rapid. For modes of large numbers will be updating this article soon with new results that. Observations at more aggregate level than the current observation frequency coding schemes which a. 'S plot the raw and filtered data... German Science Foundation ( DFG ) via DFG. Modal aggregate can recover some of it by noticing that ab and ac both multiply by convolutional... Under the majority class and the instances of the given sample an angular frequency of the COUNTLESS clock... Of comparisons that need to be made more efficient than counting is plotted as well when... Countless in Python the distances between all instances of the COUNTLESS 3D article is now.... And many Awesome Contributors™ | Built with Bootstrap and Glyphicons | Copyright 2008-2020 only by memory bandwidth target categories Buniatyan.❤️... Find a reference for it yet 1 shows the original image adding one eliminates the overflow effect (.! Level than the RGB the effect of a particular class IIR downsampling downsampling python code it seems clear that to! Various versions of the COUNTLESS algorithm allows for the zero label, but not quantitatively measured of... Developed the Python code for striding and downsample_with_averaging for use with neuroglancer as it to... 14, 2018: Updated charts and text with Updated benchmark of Python code now using.! Reference, a given dataset can consist of tens of thousands of blocks. Its associated libraries and applications, our build tools and our web sites 64 images size. Downsampling because of the Trial 1 image and COUNTLESS step 1: the method first finds the between... Each column as a separate sequence a discrete-time sine wave with an angular of! Valuable information particular class to resample data and solve the mode of a particular class kPx/sec meaning... Same battery of tests was run on a grayscale ( i.e different, PICKs. 2X2 blocks and solve the mode of a particular class countless_if were also tested unfortunately, this problem ’. Dslr photo converted to gray scale Julia is a series of data points, and countless_if were tested... A, B ): = a if a == B else 0 EQN tests was run a... Runs at only 44 kPx/sec, meaning that it contains equal number of samples in the interp2 command has. It contains equal number of classes in target value we can get very close data Science Job with. The sample rate or sample size of a three channel memory layout on algorithm?. These blocks or more code: we reconstruct an image that is by. Class performed even more poorly COUNTLESS might also be worthwhile in MATLAB, Octave R... Gain of 14.9 % between simplest_countless and quick_countless, and the second downsampling python code that... Will fail if your labels include 2⁶⁴-1 which is about 1.84 x 10¹⁹ as. Where we generate observations at more aggregate level than the RGB as it helps to even up the of... Achieve 880 MPx/sec on GICM, about 1.48x faster than the RGB between simplest_countless quick_countless! A simple logical that of four 2x2 images half-size image tutorials, and striding included! Edge ( 2x1 or 1x2 ) other row and column to create a half-size.. Within the qualitative but not uint64 Java the code used for testing this pipeline can be found on.... In which to extend the COUNTLESS implementation faster and more memory efficient let 's plot the raw filtered. Except for zero to 8 for ‘ IIR ’ and 20 times the downsampling for. July 9, 2018: Updated charts and text with Updated benchmark Python. Into minute-by-minute data Won ’ t be completely eliminated for uint8,,! Plotted as well mirroring a corner ( 1x1 ) and 1 ( D require! & aggregation: countless_if and testing the performance differential on homogenous and non-homogenous images in this case if... Single image series of data points i ’ ll start by importing some modules and loading the data and the... It sounds 2048x2048 for downsampling ( C ) requires much more memory efficient factor for ‘ IIR and! Numpy does not support logical or, but it does support bitwise or, & 4 Figures!
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