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Scientific Computing
bioimage_team
CourseMaterialImageAnalysis
Commits
3f9c89ef
Commit
3f9c89ef
authored
Mar 04, 2019
by
rhaase
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added the ImageJ macro course from January 2017
parent
0dc24bb5
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/demo_cheat_sheet.docx
...riables_StringManip_If_ForLoop/demo/demo_cheat_sheet.docx
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-0
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/test_arrays.ijm
...ion_Variables_StringManip_If_ForLoop/demo/test_arrays.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/test_loop.ijm
...ction_Variables_StringManip_If_ForLoop/demo/test_loop.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/test_strings.ijm
...on_Variables_StringManip_If_ForLoop/demo/test_strings.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/troubleshooting_error_message.ijm
...ngManip_If_ForLoop/demo/troubleshooting_error_message.ijm
+5
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/troubleshooting_tracing.ijm
...s_StringManip_If_ForLoop/demo/troubleshooting_tracing.ijm
+10
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/arrays.ijm
...tion_Variables_StringManip_If_ForLoop/examples/arrays.ijm
+27
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/blobs.gif
...ction_Variables_StringManip_If_ForLoop/examples/blobs.gif
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/code_highlights.ijm
...ables_StringManip_If_ForLoop/examples/code_highlights.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/custom_functions.ijm
...bles_StringManip_If_ForLoop/examples/custom_functions.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/dealing_with_errors.ijm
...s_StringManip_If_ForLoop/examples/dealing_with_errors.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_analyse_folder_solution.ijm
..._If_ForLoop/examples/exercise_analyse_folder_solution.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_cubic_root.ijm
...s_StringManip_If_ForLoop/examples/exercise_cubic_root.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_cubic_root_solution.ijm
...anip_If_ForLoop/examples/exercise_cubic_root_solution.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_for_loop.ijm
...les_StringManip_If_ForLoop/examples/exercise_for_loop.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_for_loop_solution.ijm
...gManip_If_ForLoop/examples/exercise_for_loop_solution.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_german_grading_system_solution.ijm
...Loop/examples/exercise_german_grading_system_solution.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_join.ijm
...riables_StringManip_If_ForLoop/examples/exercise_join.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_join_solution.ijm
...tringManip_If_ForLoop/examples/exercise_join_solution.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_math.ijm
...riables_StringManip_If_ForLoop/examples/exercise_math.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_math_solution.ijm
...tringManip_If_ForLoop/examples/exercise_math_solution.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_reading.ijm
...bles_StringManip_If_ForLoop/examples/exercise_reading.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_string_manipulation.ijm
...anip_If_ForLoop/examples/exercise_string_manipulation.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_string_manipulation_solution.ijm
...orLoop/examples/exercise_string_manipulation_solution.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/first_example.ijm
...riables_StringManip_If_ForLoop/examples/first_example.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/good_comments.ijm
...riables_StringManip_If_ForLoop/examples/good_comments.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/image_statistics.ijm
...bles_StringManip_If_ForLoop/examples/image_statistics.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/mandelbrot.ijm
..._Variables_StringManip_If_ForLoop/examples/mandelbrot.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/math_with_strings.ijm
...les_StringManip_If_ForLoop/examples/math_with_strings.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/process_folder.ijm
...iables_StringManip_If_ForLoop/examples/process_folder.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/quiz_formatting1.ijm
...bles_StringManip_If_ForLoop/examples/quiz_formatting1.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/read_image_properties.ijm
...StringManip_If_ForLoop/examples/read_image_properties.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/repetition.ijm
..._Variables_StringManip_If_ForLoop/examples/repetition.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/repetition2.ijm
...Variables_StringManip_If_ForLoop/examples/repetition2.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/return_values.ijm
...riables_StringManip_If_ForLoop/examples/return_values.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/string_replace.ijm
...iables_StringManip_If_ForLoop/examples/string_replace.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/string_variables.ijm
...bles_StringManip_If_ForLoop/examples/string_variables.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/troubleshooting_error_messages.ijm
...ip_If_ForLoop/examples/troubleshooting_error_messages.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/troubleshooting_tracing.ijm
...ringManip_If_ForLoop/examples/troubleshooting_tracing.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/troubleshooting_types.ijm
...StringManip_If_ForLoop/examples/troubleshooting_types.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/variables.ijm
...n_Variables_StringManip_If_ForLoop/examples/variables.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/yin_yang.ijm
...on_Variables_StringManip_If_ForLoop/examples/yin_yang.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/ex1-prepareImageForPresentation/prepareImageForPresentation_v1.ijm
...reImageForPresentation/prepareImageForPresentation_v1.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/ex1-prepareImageForPresentation/prepareImageForPresentation_v2.ijm
...reImageForPresentation/prepareImageForPresentation_v2.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/ex2-t1headAverageSignal.ijm
..._2017-01/2_MacroRecorder/code/ex2-t1headAverageSignal.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/ex2-t1headAverageSignal/ex2-t1headAverageSignal.ijm
.../code/ex2-t1headAverageSignal/ex2-t1headAverageSignal.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/ex4-VesiclesNucleiTimeAnalysis.ijm
...1/2_MacroRecorder/code/ex4-VesiclesNucleiTimeAnalysis.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/tuto-1-CellCounting/cellCounting_batch.ijm
...oRecorder/code/tuto-1-CellCounting/cellCounting_batch.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/tuto-1-CellCounting/cellCounting_for1Image.ijm
...order/code/tuto-1-CellCounting/cellCounting_for1Image.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/tuto-1-CellCounting/cellCounting_function_batch.ijm
.../code/tuto-1-CellCounting/cellCounting_function_batch.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/tuto-2-StackMeasures/stack_measures.ijm
...acroRecorder/code/tuto-2-StackMeasures/stack_measures.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/tuto-2-StackMeasures/stack_measures_functions.ijm
...er/code/tuto-2-StackMeasures/stack_measures_functions.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/tuto-3-complex macro/cellSegmentationFromNuclei.ijm
.../code/tuto-3-complex macro/cellSegmentationFromNuclei.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/tuto-3-complex macro/merging_example0.ijm
...roRecorder/code/tuto-3-complex macro/merging_example0.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/code/tuto-3-complex macro/merging_example1.ijm
...roRecorder/code/tuto-3-complex macro/merging_example1.ijm
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate11_C02_4.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate11_C03_1.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate15_D02_5.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate16_D02_2.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate21_C02_5.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate21_D02_3.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate23_C04_5.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate23_C05_1.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate24_C10_1.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate24_D02_3.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate24_D04_5.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate24_D05_1.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate24_D06_2.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate24_E10_3.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate25_B03_1.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate25_B03_6.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate25_B05_3.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/2D_cells_DS2/Plate25_B09_7.tiff
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ImageJMacro_24h_2017-01/2_MacroRecorder/images/mitosis.tif
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ImageJMacro_24h_2017-01/3_GUI_Parameters/demo/demo_cheat_sheet.docx
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ImageJMacro_24h_2017-01/3_GUI_Parameters/exmples/dry.ijm
ImageJMacro_24h_2017-01/3_GUI_Parameters/exmples/dry.ijm
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ImageJMacro_24h_2017-01/3_GUI_Parameters/exmples/exercise_FRAPanalysis_solution.ijm
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ImageJMacro_24h_2017-01/3_GUI_Parameters/exmples/exercise_FRAPanalysis_solution2.ijm
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ImageJMacro_24h_2017-01/3_GUI_Parameters/exmples/exercise_parameters_solution.ijm
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ImageJMacro_24h_2017-01/3_GUI_Parameters/exmples/exercise_parameters_solution2.ijm
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ImageJMacro_24h_2017-01/3_GUI_Parameters/exmples/exercise_result_tables_solution.ijm
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ImageJMacro_24h_2017-01/3_GUI_Parameters/exmples/exercise_roi_manager_solution.ijm
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ImageJMacro_24h_2017-01/3_GUI_Parameters/exmples/exercise_waitforuser_solution.ijm
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ImageJMacro_24h_2017-01/3_GUI_Parameters/exmples/overlays.ijm
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ImageJMacro_24h_2017-01/3_GUI_Parameters/exmples/parameters.ijm
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ImageJMacro_24h_2017-01/3_GUI_Parameters/exmples/waitforuser.ijm
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ImageJMacro_24h_2017-01/Cover sheet.docx
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/test_arrays.ijm
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print("\\Clear");
array = newArray(0, 1, 2);
// print (array);
// save as ijm
Array.print(array)
array[0] = 5
Array.print(array)
sum = array[0] + array[1] + array[2];
print(sum)
animals = newArray("dog", "cat");
conc = Array.concat(array, animals);
Array.print(conc);
// ----------------------------
\ No newline at end of file
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/test_loop.ijm
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start = 5;
end = 25;
print("\\Clear");
// ... many empty lines
for (i = start; i >= end; i++) {
if (i > 5) {
print("i was " + i);
}
}
\ No newline at end of file
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/test_strings.ijm
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print("\\Clear");
firstname = "Robert";
lastname = "Haase";
name = firstname + " " + lastname;
print (name);
//------------------------------------------
a = "1";
b = 1;
sumAB = a + b;
sumBA = b + a;
print(sumAB);
print(sumBA);
//------------------------------------------
print("\\Clear");
text = "Hello world!";
text = replace(text, "world", "universe");
print(text);
\ No newline at end of file
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/troubleshooting_error_message.ijm
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Sentence = "Can you can a can as a canner can can a can?";
if (startsWith(Sentence, "Can") {
print(sentence);
}
\ No newline at end of file
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/demo/troubleshooting_tracing.ijm
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start = 0;
end = 10;
// print numbers
for ( i = start; i < end; i++ ) {
if (i > 5) {
print(i);
}
}
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/arrays.ijm
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// numeric arrays
v = newArray(3, -4, 0);
Array.print(v);
// create an array with three elements containing zeros
v = newArray(3);
Array.print(v);
// manipulate arrays
v[0] = 3.5
Array.print(v);
// access array elements
print( v[2] );
// string arrayss
animals = newArray("dog", "cat", "mouse");
// combining arrays
mixed = Array.concat(v, animals);
Array.print(mixed);
// get length of an array
numberOfElements = lengthOf(v);
print("v has " + numberOfElements + " elements");
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/code_highlights.ijm
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a = 5;
b = 7;
sum = a + b;
ratio = a / b;
print("The sum is + sum);
print("The ratio is " + ratio);
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/custom_functions.ijm
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// point 1
x1 = 3;
y1 = 5;
// point 2
x2 = 7;
y2 = 8;
// point 3
x3 = 14;
y3 = 3;
printDistance(x1, y1, x2, y2, "between 1 and 2");
printDistance(x2, y2, x3, y3, "between 2 and 3");
printDistance(x1, y1, x3, y3, "between 1 and 3");
function printDistance(xA, yA, xB, yB, description) {
d = sqrt(pow(xA - xB, 2) + pow(yA - yB, 2));
print("The distance " + description + " is " + d);
}
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/dealing_with_errors.ijm
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_analyse_folder_solution.ijm
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// initialise program
foldername = "/Users/rhaase/temp/";
// get all files in the folder as list
list = getFileList( foldername );
// print out the list; item by item
for (i = 0; i < lengthOf(list); i++) {
filename = list[i];
if (endsWith(filename, ".tif") ||
endsWith(filename, ".gif")) {
open(foldername + filename);
// analyse FOV
getDimensions (imageWidth, imageHeight,
channels, slices, frames);
getPixelSize (physicalUnitName,
pixelWidth, pixelHeight);
// calculate FOV size
FOVwidth = (imageWidth * pixelWidth);
FOVheight = (imageHeight * pixelHeight);
// show results
print(filename);
print("FOV width: " + FOVwidth + physicalUnitName);
print("FOV height: " + FOVheight + physicalUnitName);
close();
}
}
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_cubic_root.ijm
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// call build-in function
variable1 = pow(2, 3);
// call custom function
variable2 = cubicRoot(variable1);
print(variable2);
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_cubic_root_solution.ijm
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// call build-in function
variable1 = pow(2, 3);
// call custom function
variable2 = cubicRoot(variable1);
print(variable2);
// define a self-made custom function
function cubicRoot(x) {
return pow(x, 1 / 3);
}
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_for_loop.ijm
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print("\\Clear");
foldername = "/Users/rhaase/temp/";
filelist = getFileList(foldername);
for ( i = 0; i < lengthOf(filelist); i++) {
imagefilename = filelist[i];
if (endsWith(imagefilename, ".tif")) {
print(imagefilename);
}
}
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_for_loop_solution.ijm
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// initialisation
input_num = getNumber("Input a number", 5);
// print 10 numbers
for( i = input_num; i >= 0 ; i-- ){
print(i);
}
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_german_grading_system_solution.ijm
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// initialise program
numberOfTotalPoints = 50;
numberOfReachedPoints_Robert = 40;
// calculate percentage
percentage = numberOfReachedPoints_Robert / numberOfTotalPoints * 100;
// print out grade
if (percentage >= 90) {
print("very good");
}
if (percentage >= 80 && percentage < 90) {
print("good");
}
if (percentage >= 65 && percentage < 80) {
print("satisfactory");
}
if (percentage >= 50 && percentage < 65) {
print("sufficient");
}
if (percentage > 0 && percentage < 50) {
print("insufficient");
}
if (percentage == 0) {
print("failed");
}
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_join.ijm
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sentence = "Text processing is a pain.";
words = split(sentence, " ");
words[0] = "Image";
words[4] = "big fun.";
sentence = join(words, " ");
print(sentence);
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_join_solution.ijm
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sentence = "Text processing is a pain.";
words = split(sentence, " ");
words[0] = "Image";
words[4] = "big fun.";
sentence = join(words, " ");
print(sentence);
// take an array and concatenate is elements.
// Put a separator between the elments.
function join(array, separator) {
result = "";
for (i = 0; i < lengthOf(array); i++) {
// put the separator not before the first element.
if (i > 0) {
result += separator;
}
result += array[i];
}
return result;
}
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_math.ijm
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// initialise program
x1 = 3;
y1 = 5;
x2 = 7;
y2 = 8;
// run complicated algorithm
d =
// show the result
print("The distance is " + d);
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_math_solution.ijm
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// initialise program
x1 = 3;
y1 = 5;
x2 = 7;
y2 = 8;
// run complicated algorithm
d = sqrt(pow(x1 - x2, 2) +
pow(y1 - y2, 2));
// show the result
print("The distance is " + d);
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_reading.ijm
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sentence = "double bubble gum bubbles double";
words = split(sentence, " ");
temp = words[0];
words[0] = words[4];
words[4] = temp;
sentence = join(words, " ");
print(sentence);
function join(array, separator) {
result = "";
for (i = 0; i < lengthOf(array); i++) {
if (i > 0) {
result += separator;
}
result += array[i];
}
return result;
}
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_string_manipulation.ijm
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// retrieve filename
filename = "blobs_timepoint5_conditionB.gif";
// cut out interesting parts
filenameParts = split(filename, "_");
timepoint = filenameParts[1];
// remove unneccessary characters
timepoint = replace(timepoint, "timepoint", "");
// show result
print("Timepoint was: " + timepoint);
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/exercise_string_manipulation_solution.ijm
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// retrieve filename
filename = "blobs_timepoint5_conditionB.gif";
// cut out interesting parts
filenameParts = split(filename, "_");
timepoint = filenameParts[1];
condition = filenameParts[2];
// remove unneccessary characters
timepoint = replace(timepoint, "timepoint", "");
condition = replace(condition, "condition", "");
condition = replace(condition, ".gif", "");
// show result
print("Timepoint was: " + timepoint);
print("Condition was: " + condition);
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/first_example.ijm
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//
// This program is our first example
//
// Author: Robert Haase, MPI-CBG,
// rhaase@mpi-cbg.de
// July 2015
print("Hello world");
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/good_comments.ijm
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// This program is our second example.
// It sums up two numbers.
//
// Usage:
// * Run it in FIJI (www.fiji.sc)
//
// Author: Robert Haase, MPI CBG,
// rhaase@extern.mpi-cbg.de
// July 2016
// initialise program
a = 1;
b = 2.5;
// run complicated algorithm
final_result = a + b;
print( final_result );
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/image_statistics.ijm
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// initialise program
imageFilename = "blobs.gif";
open( imageFilename );
// get image statistics
getStatistics(area, mean, min, max, std);
// show results
print("The grey value ranges from " + min + " to " + max + ". ");
print("It has an average of " + mean + " +- " + std + ". ");
close();
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/mandelbrot.ijm
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window_size = 300;
max_size = 4;
max_iterations = 64;
speed = 0.95;
imin = -1.25;
imax = 1.25;
rmin = -1.5;
rmax = 1;
title = "Suprise"
newImage(title, "32-bit", window_size, window_size, 1);
count = 0;
while (isOpen(title)) {
imin = imin * speed;
imax = imax * speed;
rmax = rmin + (rmax-rmin) * speed;
deltar=(rmax-rmin)/(window_size-1);
deltai=(imax-imin)/(window_size-1);
arr = newArray(window_size * window_size);
count = 0;
for (row=0; row<window_size; row++) {
for (col=0; col<window_size; col++) {
x=0;
y=0;
ci=(imin+row*deltai);
cr=(rmin+col*deltar);
color=0;
do {
color++;
xsq=x*x;
ysq=y*y;
if ((xsq+ysq)<(max_size)) {
y=x*2*y+ci;
x=xsq-ysq+cr;
}
}
while ((color<max_iterations)&&((xsq+ysq)<(max_size)));
if (color>=max_iterations) {
color=0;
}
arr[count] = color;
count++;
}
}
count = 0;
for (row=0; row<window_size; row++) {
for (col=0; col<window_size; col++) {
if (isOpen(title)) {
setPixel (col, row, arr[count]);
}
count++;
}
}
if (isOpen(title)) {
run("6 shades");
updateDisplay();
run("Enhance Contrast", "saturated=0.35");
}
count ++;
}
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/math_with_strings.ijm
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// initialise program
a = "1";
b = 1;
// calculate the sum
sumAB = a + b;
sumBA = b + a;
// show the result
print("The sumAB is " + sumAB);
print("The sumBA is " + sumBA);
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/process_folder.ijm
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// initialise program
foldername = "/Users/rhaase/temp/";
// get all files in the folder as list
list = getFileList( foldername );
// print out the list; item by item
for (i = 0; i < list.length; i++) {
filename = list[i];
print( filename );
}
ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/quiz_formatting1.ijm
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measurements = newArray(34,67,32,9,22,37,22,5,12,78,51);
threshold=50;count=0;
minimum=measurements[0];maximum=measuremnts[0];
for (i=0;i<lengthOf(measurements);i++){
if(measurements[i]>threshold){count++;}
if(measurements[i]<minimum){minimum=measurements[i]}
if(measurements[i]>maximum){maximum=measurements[i]}
}
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ImageJMacro_24h_2017-01/1_Introduction_Variables_StringManip_If_ForLoop/examples/read_image_properties.ijm
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// initialise program
imageFilename = "blobs.gif";
open( imageFilename );
// read image properties
width = getWidth();
height = getHeight();
getPixelSize(unit, pixelWidth, pixelHeight);