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1. This defines the boreholes horizontal resolution In a borehole image it describes how many pixels were captured at every row down the borehole Borehole Core depth mm This gives the total depth of the borehole or core in millimetres Start depth mm This gives the start depth of the borehole or core in millimetres End depth mm This gives the end depth of the borehole or core in millimetres 3 1 2 Options A number of options can be configured from the menu bar 3 1 2 1 Auto save project By default every change that is made to your annotation automatically saves so that there is no need to manually save regularly To turn this off on the menu bar select Options gt Auto save project 3 1 2 2 Show hide features Once features have been added either manually or automatically there is an option to hide them in order to view the borehole core image To show or hide features select the Show features tick box below the Features buttons box Figure 5 Inclusions PI Fluid Lewel Show Features Figure 5 The features buttons box and the show hide features tick box 3 2 Layers Layers are the main feature which can be annotated with the feature annotation tool In borehole projects layers appear as sinusoids Figure 6 and in core projects they can be added as straight sloped lines y depth p_sin x 6 7 x azimuth Xe x p amplitude 8 phase Figure 6 Image illustrating how a layers
2. belong to actual layers as opposed to other artefacts Edges are grouped together based on their position and size and kept only if they meet certain criteria In simplified mode two edge processing options can be altered Link edges length pixels This determines how many pixels long an edge must be before it is considered for linking with other smaller edges Remove edges length pixels This determines how many pixels long an edge must be in order for it not to be discarded 3 2 1 2 Advanced mode By Automatic layer detection parameters Canny edge detector High threshold pixels Low threshold pixels Gaussian width pixels Gaussian sigma preels Horizontal weighting Vertical weighting Edge processing Link edges length pocels 120 Link edges distance pels 7 Remove edges length pels 180 Join edges distance picela 10 Frocess Start M 4 42 End M 24 32 O Whole borehole Disable layer detection Figure 8 Automatic layer detection parameters in advanced mode 3 2 1 2 1 Canny Edge Detector The Canny edge detector deals with finding edges in the image There are four parameters for this two dealing with the filter size and two with thresholds for determining when an edge is considered strong enough High threshold pixels The high threshold of the feature determining how strong an edge must be Low threshold pixels The low threshold of the feature determining h
3. debris 4 Custer Type Coarse Debris False Diamicton False Fine Debris True Large Bubbles False Small Bubbles False 4 Depth End Depth mm 249372 Start Depth mm 24949 4 Points Points 165 22977 256 229777 21 Start Depth mm The clusters start depth in millimetres Figure 16 The Cluster properties bar 3 3 6 1 Fixed properties Depth Start Depth mm The depth of the start of the cluster in millimetres End Depth mm The depth of the start of the cluster in millimetres Points The points joining the cluster s edges 3 3 6 2 Variable properties Description A string of text describing the cluster Cluster Type A number of values can be set to true or false depending on whether the cluster contains the listed material These are Coarse debris Diamicton Fine debris Large bubbles and Small bubbles 3 4 Inclusions 3 4 1 Adding an inclusion Inclusions can be manually annotated onto the image by selection the Add Inclusion button 8 and left clicking points around the inclusion To finish annotating the inclusion left click the first point again This will close the annotated shape Figure 17 b Figure 17 Adding an inclusion a The original image b Adding the inclusion c Completed inclusion 3 4 2 Editing an inclusion The Edit Inclusion button Sallows for the repositioning of the entire annotated inclusion or individual added points Once a
4. initially opened either the Create new borehole project from image file or the Create new ice core project from image file button can be selected from the project action dialog box Figure 1 It is also possible to create this project type from the menu by choosing File gt New gt From Image gt and either Borehole image or Core image Similarly the New icon H can be clicked from the menu bar and From image gt then Borehole image or Core image selected Once this has been selected an open file dialog box will appear Locate and highlight the relevant bitmap file and click the Open button Borehole details Borehole name Ta DML10_02 12 10_BHO2_up1 30 0 30 9 Start Depth mm 0 End Depth mm Depth Resolution Project a S 1a DML10_02 12 10_BHO2_up1 30 0 30 9 _Annotation 19 04 2012 1346 Froject location CAUsers im Desktop TEST SPACE FOR ANNOTATION TOOL Browse Figure 2 New Project from image dialog box A new dialog box will open Figure 2 The text fields are automatically populated using details from the selected bitmap Borehole core name This is set to the same as the bitmap file title although this can be changed to any value Start depth mm This is set to O It can be set to any valid integer value positive or negative When this value is changed the end depth value is automatically updated End depth mm This is set to th
5. of more than one edge this can be annotated by either drawing the other edge and joining the two or by using either the Alter thickness of layer section 3 2 2 1 2 or Alter one edge of layer section 3 2 2 1 3 button 3 2 2 1 2 Altering layer thickness With a layer selected left click the Alter thickness of layer button S By holding down the left mouse button and dragging either of the edges up or down the layer thickness can be altered 3 2 2 1 3 Altering a layer The Alter layer button AX allows a layer to be moved and its amplitude changed When a layer is selected the Alter layer button is automatically activated otherwise it can be selected by left clicking the button To move the layer hover the mouse pointer over the layer until it changes to the move icon then hold down the left mouse button and drag to move the vertical and horizontal position of the layer To change the layers amplitude hover the mouse pointer over the lowest point of the sinusoid until it changes to the north south icon I then hold down the left mouse button and drag either up or down to alter the amplitude 3 2 2 1 4 Altering one edge of layer The Alter one edge of layer button SS allows for the one edge of a multi edge layer to be moved and its amplitude altered To alter one edge of a layer left click the Alter one edge of layer button and follow the steps in section 3 2 2 1 3 above 3 2 2 1 5 De
6. ABERYSTWYTH UNIVERSITY Borehole and Ice Feature Annotation Tool User Manual Version 1 0 Terry Malone trm8 aber ac uk Introduction Borehole and Ice Feature Annotation Tool aids in the annotation and classification of borehole features including layers clusters and inclusions It works with optical televiewer images of glacier borehole images 1 Installation The standalone version of Borehole and Ice Feature Annotation Tool requires no installation To start the software open the file FeatureAnnotationTool exe in the program folder There are a number of required library files also located in this folder If any of these are moved or deleted or if the FeatureAnnotationTool exe file is moved parts of the software will not function correctly 2 Getting started 2 1 Projects Each project creates a folder where all files relating to the annotation are located There are three options available for creating a new project Create a new borehole project from a bitmap file create a new ice core project from a bitmap file and create a new project from HED otv files Select Action Create new borehole project from image file Create new ice core project from image file Create new project from otv file Open existing project Figure 1 The project selection dialog box 2 1 1 Create a new borehole core project from a bitmap There are a number of ways this type of project can be created When the software is
7. amework must be installed on the machine If this is not the case an error message Figure 24 may be displayed when attempting to start the software FeatureAnnotation ool exe NET Framework Initialization Error To run this application you First must install one of the Following versions of the NET Framework 4 0 30319 Contact your application publisher for instructions about obtaining the appropriate version of the NET Framework Figure 24 NET Framework Initialization Error The latest version of the NET Framework can be obtained for free from For further support or to report any bugs please send an email to Terry Malone at trm8 aber ac uk giving as much detail as possible regarding the issue
8. can be clicked from the menu bar and From otv hed gt selected Once this has been selected an open file dialog box will appear Locate and highlight the relavent hed file ensuring that the corresponding otv file is in the same folder Project E DML10_02 12 10_ BHO2_down1_Annotation 23 04 2012 15 49 55 Project location C Users trm8 Desktop Browse Figure 3 New project from otv hed file dialog box A new dialog box will open Figure 3 The text fields are automatically populated using details from the selected files Project name This defines the name of the project folder and is set to hed file title Annotation date This can be changed to any value that does not contain any invalid filename characters lt gt Project Location This shows where the project folder will be located Its default value is the location of the selected file but it can be changed to any valid folder location Alternatively by clicking the Browse button a location can be selected using a folder selection dialog box When creating a project from an otv hed file there is no need to enter details such as the borehole name the start and end depths and resolution as these values are taken from the hed header file 2 1 3 Open existing project An existing project can be opened by selecting the Open existing project button from the project action dialog box Figure 1 Alternatively an ex
9. cription Description A small void Void 4 Depth Clast End Depth Bubble Start Depth 4 Points Points 166 23185 293 23162 2 Inclusion Type The type of inclusion Figure 18 The inclusion properties bar 3 4 6 1 Fixed properties Depth Start Depth mm The depth of the start of the inclusion in millimetres End Depth mm The depth of the start of the inclusion in millimetres Points The points joining the inclusion s edges 3 4 6 2 Variable properties Description A string of text describing the inclusion Inclusion Type A drop down box gives the option of selecting either Clast Bubble or Void 4 Outputs 4 1 Export image The image currently being worked on can be exported as a bitmap with a number of different options The image can be exported with or without the features drawn on with the option of adding a ruler Figure 19 To export an image from the menu bar select Tools gt Export image and select the options based on whether to show the features and ruler Figure 19 Results of exporting a borehole image a Without features and ruler b With features and no ruler c With features and ruler 4 2 Export features The details of features which have been annotated onto the image can be exported to either a text or an excel file To do this from the menu bar select Features and either Export to excel or Export to text file then select which f
10. e a cluster has been added the Edit Cluster button is automatically selected otherwise it can be selected by left clicking the button To reposition the entire annotated cluster hold down the left mouse button anywhere within the shaded area and drag the shape to the desired location To alter any of the individual cluster points hold down the left mouse button within the square Figure 15c and drag the point to the desired location 3 3 3 Adding a point to a cluster Once a cluster has been annotated additional points can be added by selecting the Add Point to Selected Cluster button and left clicking on or close to the line surrounding the cluster shape 3 3 4 Removing a point from a cluster Once a cluster has been annotated points can be removed by selecting the Remove Point from Selected Cluster button A and left clicking the square surrounding the point to be removed Note that there can be no less than three points representing a cluster 3 3 5 Deleting a cluster When a cluster is selected it can be deleted by left clicking the Delete Cluster button no or pressing the Delete key on the keyboard 3 3 6 Cluster properties A number of the cluster s properties are displayed in BIFAT s properties bar Figure 16 Some of these can be altered by the user while others are fixed and can only be changed by direct manipulation of the cluster itself J 4 Description Description Cluster of fine
11. e height of the image in pixels It can be set to any valid integer value positive or negative When this value is changed the start depth value is automatically updated Depth Resolution this defines the resolution of the image in mm per pixels and is automatically set to 1 This can be changed to any positive integer value The value of end depth will automatically be updated to reflect this change Project name This defines the name of the project folder and is set to Bitmap file title Annotation date This can be changed to any value that does not contain any invalid filename characters lt gt Project Location This shows where the project folder will be located It s default value is the location of the selected borehole image but it can be changed to any valid folder location Alternatively by clicking the Browse button a location can be selected using a folder selection dialog box Once the correct values have been entered click on the OK button to load the image into the project 2 1 2 Create anew project from otv hed files There are a number of ways this type of project can be created When the software is initially opened the Create new file from otv file button can be selected from the project action dialog box Figure 1 It is also possible to create this project type from the menu by choosing File gt New gt From otv hed gt or similarly the New icon H
12. eatures to export If selecting to export to excel the option of exporting all features is available saving layers clusters and inclusions to separate worksheets Once a selection has been made a window will open allowing for the selection of which of the features details are to be exported Figure 20 Figure 21 and Figure 22 For a detailed description of each of the details see sections 3 2 3 Layer properties 3 3 6 Cluster properties and 3 4 6 Inclusion properties for layers clusters and inclusions respectively If selecting to export layer details the option of exporting mean layer brightness is available This option calculates the mean brightness between the edges of two edge layers on a scale of 0 255 with 0 bwing black and 255 being white Note that in an image with a number of layers selecting this option may cause the writing of the file to take a long time Figure 20 Layer details to export Ba Cluster details to export Figure 21 Cluster details to export Buy Inclusion details to export Properties to export Start depth mm End depth mm Top Y boundary Bottom Y boundary left X boundary Right X boundary Points Inclusion type Inclusion description Figure 22 Inclusion details to export 4 3 Depth Luminosity profile A luminosity profile of the borehole core can also be created and written to an Excel or text file The depth luminosity profile gives a row by row average of brightness intensi
13. intersect a borehole A and how they appear on the unrolled image B 3 2 1 Automatic layer detection To begin automatic layer detection select Automatic detection gt Detect layers from the menu The automatic layer detection parameters dialog box will appear Initially the box is set to simplified parameters This allows for more general settings to be applied In advanced mode there are more parameters to modify giving more control 3 2 1 1 Simplified mode Canny edge detector Filter size pixels Edge processing Link edges length pixels Remove edges length pixels Start M 432 End M 24 32 Whole borehole Disable layer detection Advanced Options Figure 7 Automatic layer detection parameters in simplified mode 3 2 1 1 1 Canny Edge Detector The Canny edge detector deals with finding edges in the image There are four parameters for this two dealing with the filter size and two with thresholds for determining when an edge is considered strong enough In simplified mode only one parameter relating to the edge detector can be edited Filter size pixels This determines the width of the filter The sigma value of the filter will automatically be set to a third of the chosen value The two threshold values are automatically set to values which generally perform well 3 2 1 1 2 Edge Processing Once edges have been detected they are then processed in order to determine if they
14. ints that are far apart Figure 11 A sloped line will be annotated onto the core image Figure 11 Adding a layer to a core image a Left click two points along the line b A sloped line will be automatically drawn onto the image If a layer consists of more than one edge this can be annotated by either drawing the other edge and joining the two or by using either the Alter thickness of layer section 3 2 2 2 2 or Alter one edge of layer section 3 2 2 2 3 3 2 2 2 2 Altering layer thickness With a layer selected left click the Alter thickness of layer button E Hold down the left mouse button and drag either of the edges up or down the layer thickness can be altered 3 2 2 2 3 Altering a layer In a core image the Alter layer button EE allows a layer to be moved When a layer is selected the Alter layer button is automatically activated otherwise it can be selected by left clicking the button To move the layer hover the mouse pointer over the layer until it changes to the move icon ep then hold down the left mouse button and drag to move the vertical and horizontal position of the layer Altering one edge of layer The Alter one edge of layer button AS allows for the one edge of a multi edge layer to be moved To alter one edge of a layer left click the Alter one edge of layer button and follow the steps in section 3 2 2 1 3 above 3 2 2 2 4 Deleting a layer ae When a layer i
15. isting project can be opened choosing the menu option File gt Open gt or by selecting the Open icon a from the menu bar An open dialog box will appear and the relevant features file can be selected Alternatively the features file can be double clicked from out with the Feature Annotation Tool and the software will be launched and the current project opened 3 Annotating Features 3 1 General 3 1 1 Borehole Core Details To view details of the current project select Tools gt Borehole details or Tools gt Core details This will open a window displaying the details of the project Figure 4 Borehole name NEEM_30 7 10_down3 Depth resolution 1 Azimuth resolution f20 Borehole depth mm 618961 Start depth mm 11003 End depth mm 629964 Figure 4 The Borehole details window The details that are displayed are Borehole Core name This gives the name of the borehole or core The default value is the name of the file if the project was created from an image and can be changed when creating the project If the project was created from an otv file the borehole name is taken from the header file and can not be altered Depth resolution This defines the vertical resolution of the image in millimetres per pixel This is set manually when creating a new project from an image and is automatically read from the header file when creating a new project from an otv file Azimuth Resolution
16. leting a layer OO ae When a layer is selected it can be deleted by left clicking the Delete layer button pressing the Delete key on the keyboard or right clicking the layer and selecting Delete 3 2 2 1 6 Joining and splitting a layer Once automatic layer detection has been carried out or in the course of manually annotating layers some annotated edges may need to be combined to form layers Figure 10 or layers split to form individual edges Figure 10 Image showing the joining of layers a The original image b The image with annotated layers c The image after the top two layers are merged into one Joining To join two edges together first left click to select one of the edges then while holding down the control key left click the layer it is to be joined to These edges will be joined to form one layer The end layer will take the properties of the first selected edge Splitting With a layer selected hold down the shift key and left click anywhere in the layer This will split the layer into two separate one edge layers with both taking the properties of the original layer 3 2 2 2 Core Image A core layer differs from a borehole layer in that it s edges are represented by a sloped line rather than a sinusoid 3 2 2 2 1 Adding a layer aN To add a layer to a core image select the Add layer button then left click two points along the edge For best results select po
17. llimetres Top Edge Intercept mm The depth in millimetres where the top edge intersects the y axis Slope The slope of the top edge Bottom Edge Intercept mm The depth in millimetres where the bottom edge intersects the y axis Slope The slope of the bottom edge 3 2 3 2 Variable properties A number of the layer s properties can be directly edited in the properties bar These are optional and can be left at the default values Description A string of text describing the layer Group The group the layer belongs to see section 3 2 4 Layer groups for further information Quality The visibility of the layer 1 very poor 4 very clear Layer Type A number of values can be set to true or false depending on whether the layer contains the listed material These are Clean Coarse debris Diamicton Fine debris Large bubbles Small bubbles and Void 3 2 4 Layer groups Layers can be categorised as belonging to different groups making performing later analysis on them easier When a layer is created it is automatically classed as belonging to the group Unspecified There are two ways to add a new group The first is to type a new group name in the layer s property grid box The second way is to open the Layer groups dialog box Figure 14 by selecting Features gt Layers gt Groups from the menu strip From here press the Add group button and a dia
18. log box will appear where the new group name can be entered By Layer Groups Number of Layers in Group Debris layers Figure 14 The Layer groups dialog box A number of other actions can be carried out using the Layer groups box Delete group This button will delete the selected group Any layers belonging to this group will be added to the Unspecified group Unspecified cannot be deleted since there must always be at least one group Rename group This allows the renaming of a group after creation The Unspecified group cannot be renamed Change colour The colour that each group s layers are both in the Feature Annotation Tool and when exported as images can be changed here The group a layer belongs to can be changed in the layer s property grid or by right clicking on the layer and selecting Select Group and the group you wish to move it to 3 3 Clusters 3 3 1 Adding a cluster Clusters can be manually annotated onto the image by selection the Add Cluster button 4 and left clicking points around the cluster To finish annotating the cluster left click the first point again This will close the annotated shape Figure 15 Figure 15 Adding a cluster a The original image b Adding the cluster c Completed cluster 3 3 2 Editing a cluster The Edit Cluster button amp allows for the repositioning of the entire annotated cluster or individual added points Onc
19. n inclusion has been added the Edit Inclusion button is automatically selected otherwise it can be selected by left clicking the button To reposition the entire annotated inclusion hold down the left mouse button anywhere within the shaded area and drag the shape to the desired location To alter any of the individual inclusion points hold down the left mouse button within the square Figure 17c and drag the point to the desired location 3 4 3 Adding a point to an inclusion Once an inclusion has been annotated additional points can be added by selecting the Add Point to Selected Inclusion button Fand left clicking on or close to the line surrounding the inclusion shape 3 4 4 Removing a point from an inclusion Once an inclusion has been annotated points can be removed by selecting the Remove Point from Selected Inclusion button Z and left clicking the square surrounding the point to be removed Note that there can be no less than three points representing an inclusion 3 4 5 Deleting an inclusion When an inclusion is selected it can be deleted by left clicking the Delete Inclusion button 5 or pressing the Delete key on the keyboard 3 4 6 Inclusion properties A number of the inclusion s properties are displayed in BIFAT s properties bar Figure 18Figure 16 Some of these can be altered by the user while others are fixed and can only be changed by direct manipulation of the inclusion itself 4 Des
20. ow strong an edge must be Gaussian width pixels This determines the width and height in pixels of the Gaussian filter used Gaussian sigma pixels This determines the size of the sigma value in pixels of the Gaussian filter used 3 2 1 2 2 Edge Processing Once edges have been detected they are then processed in order to determine if they belong to actual layers as opposed to other artefacts Edges are grouped together based on their position and size and kept only if they meet certain criteria In advanced mode four edge processing options can be altered Link edges length pixels This determines how many pixels long an edge must be before it is considered for linking with other smaller edges Link edges distance pixels This determines how close in pixels the ends of edges should be to be considered for linking Remove edges length pixels This determines how many pixels long an edge must be in order for it not to be discarded Join edges distance pixels This determines how close in pixels the ends of edges must be in order to be considered for joining 3 2 1 3 Processing options The Process section sets the start and end depth of the section to be automatically processed By sliding the two scrollbars the start and end depth can be changed Alternatively there are three radio buttons which can be used to automatically set the depths Whole borehole The entire borehole is p
21. rocessed Current section The current section that is being viewed is processed Current viewing area The area in the current window is processed 3 2 1 4 Disable layer detection As well as detecting edges automatic feature detection attempts to group found edges together as layers The current version of this works well on some images but on others particularly where contrast is low results are less than desirable Tick this box if you would like to just run automatic edge detection leaving layer grouping to be carried out manually When all of the relevant options have been selected press the Run button A dialog box will pop up asking if you wish to Remove previously annotated layers This option removes any layers which have already been annotated manually or automatically in the section to be processed 3 2 2 Manual annotation On a borehole project layers can be annotated as sinusoids and on a core project they are annotated as sloped lines 3 2 2 1 Borehole Image 3 2 2 1 1 Adding a layer ae Layers can be annotated by selecting the Add layer button gt then clicking two points the highest and lowest along one of its edges Point 1 and Point 2 from Figure 9a A sinusoid will then be drawn on the image Figure 9b Figure 9 Adding a layer to a borehole image a Left click two points along the edge b A sinusoidal line will be automatically drawn onto the image If a layer consists
22. rue Coarse Debris False Diamicton False Fine Debris False Large Bubbles False Small Bubbles False Void False 4 Depth Start Depth mm 25450 End Depth mm 25532 4 Top Edge Amplitude mm 12 Azimuth 41 Depth mm 25462 4 Bottom Edge Amplitude mm 12 Azimuth Fi Depth mm 25520 Hne Debris Does the layer contain fine debris Figure 13 The layer properties bar 3 2 3 1 Fixed properties 3 2 3 1 1 Borehole layer properties Depth Start Depth mm The depth of the start of the layer in millimetres Not to be confused with the depth of each edge in the layer End Depth mm The depth of the end of the layer in millimetres Top Edge Amplitude The amplitude half the height of the top edge of the layer in millimetres Azimuth The orientation of the top edge in degrees 0 360 The azimuth point is the lowest point or trough of the edge Depth mm The depth of the top edge in millimetres Bottom Edge Amplitude The amplitude half the height of the bottom edge of the layer in millimetres Azimuth The orientation of the bottom edge in degrees 0 360 The azimuth point is the lowest point or trough of the edge Depth mm The depth of the bottom edge in millimetres 3 2 3 1 2 Core layer properties Depth Start Depth mm The depth of the start of the layer in millimetres Not to be confused with the depth of each edge in the layer End Depth mm The depth of the end of the layer in mi
23. s selected it can be deleted by left clicking the Delete layer button pressing the Delete key on the keyboard or right clicking the layer and selecting Delete 3 2 2 2 5 Joining and splitting a layer Once automatic layer detection has been carried out or in the course of manually annotating layers some annotated edges may need to be combined to form layers Figure 12 or layers split to form individual edges Figure 12 Image showing the joining of layers a The original image b The image with annotated layers c The image after the top two layers are merged into one Joining To join two edges together first left click to select one of the edges then while holding down the control key left click the layer it is to be joined to These edges will be joined to form one layer The end layer will take the properties of the first selected edge Splitting With a layer selected hold down the shift key and left click anywhere in the layer This will split the layer into two separate one edge layers with both taking the properties of the original layer 3 2 3 Layer properties A number of the layer s properties are displayed in BIFAT s layer properties bar Figure 13 Some of these can be altered by the user while others are fixed and can only be changed by direct manipulation of the layer itself EEJ 4 Description 4 Description Group Annual layering Quality 3 4 Layer Type Clean T
24. ty for the entire image To create a depth luminosity profile from the menu bar select Tools gt Create depth luminosity profile gt then select either Write to Excel or Write to text file This will open the Create depth luminosity profile window Figure 23 where a number of options are available The sample rate can be modified so that the average luminosity is not taken at every row but instead at a specified distance It is also possible to remove certain features from the profile so that for example a background only profile can be exported or a profile including just annual layering amp Create Depth Luminosity Profile i Settings Sample Rate mm Background anything not annotated All annotated features All annotated layers Uneneciied Annual layering All annotated clusters All annotated inclusions Figure 23 The depth luminosity profile creation window 5 Troubleshooting 5 1 Folder Permissions In windows 7 it is sometimes necessary to allow programs access to the folders that are being worked on If BIFAT has difficulty saving projects right click the project folder and select properties Select the Security tab and click the Edit button Make sure that the current user has acces to Write and Modify the current folder If not select the tick boxes and click the Apply button 5 2 NET Framework Initialization Error To run BIFAT an up to date version of the NET fr

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