diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..d9d6885 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,3 @@ +*.ipynb filter=nbstripout + +*.ipynb diff=ipynb diff --git a/.gitignore b/.gitignore index 4df4b39..a7dce3b 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,4 @@ .ipynb_checkpoints -.gitattributes __pycache__ *.swp +*.ziggy diff --git a/modules/module1/InClass/Index.ipynb b/modules/module1/InClass/Index.ipynb index 1726f9d..f3bb4d1 100644 --- a/modules/module1/InClass/Index.ipynb +++ b/modules/module1/InClass/Index.ipynb @@ -54,7 +54,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.2" + "version": "3.7.3" }, "latex_envs": { "LaTeX_envs_menu_present": true, diff --git a/modules/module1/InClass/Untitled.ipynb b/modules/module1/InClass/Untitled.ipynb new file mode 100644 index 0000000..97a8f8a --- /dev/null +++ b/modules/module1/InClass/Untitled.ipynb @@ -0,0 +1,47 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "\n", + "cd /home/uu00180764/DATA/Numerics/mimic2/hr/subjects\n", + "grep -lrP \"\\b(? ~/hr200.txt\n", + "cd /home/uu01080764/DATA/Numerics/mimic2/bp/subjects\n", + "grep -lrP \"\\b(? ~/bp200.txt\n", + "grep -Fx -f ~/bp200.txt ~/hr200.txt" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.3" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/modules/module1/InClass/environment_variables.ipynb b/modules/module1/InClass/environment_variables.ipynb index 65b68be..0242d2f 100644 --- a/modules/module1/InClass/environment_variables.ipynb +++ b/modules/module1/InClass/environment_variables.ipynb @@ -239,10 +239,10 @@ "outputs": [], "source": [ "%%bash\n", - "rm -r /home/jovyan/bin\n", - "mkdir /home/jovyan/bin\n", - "cp ./ls /home/jovyan/bin/.\n", - "chmod +x /home/jovyan/bin/ls" + "rm -r /home/uu00180764/bin\n", + "mkdir /home/uu00180764/bin\n", + "cp ./ls /home/uu00180764/bin/.\n", + "chmod +x /home/uu00180764/bin/ls" ] }, { @@ -252,7 +252,7 @@ "outputs": [], "source": [ "%%bash\n", - "/home/jovyan/bin/ls" + "/home/uu00180764/bin/ls" ] }, { @@ -280,9 +280,9 @@ "source": [ "%%bash\n", "\n", - "PATH=/home/jovyan/bin:$PATH\n", + "PATH=/home/uu00180764/bin:$PATH\n", "which ls\n", - "ls /home/jovyan/DATA/Misc" + "ls /home/uu00180764/DATA/Misc" ] }, { @@ -293,9 +293,9 @@ "source": [ "%%bash\n", "echo $PATH\n", - "export PATH=$PATH:/home/jovyan/bin\n", + "export PATH=$PATH:/home/uu00180764/bin\n", "which ls\n", - "ls /home/jovyan/DATA/Misc\n" + "ls /home/uu00180764/DATA/Misc\n" ] }, { @@ -307,6 +307,13 @@ "%%bash\n", "echo $PATH" ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { @@ -325,7 +332,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module1/InClass/finding_files.ipynb b/modules/module1/InClass/finding_files.ipynb index 6de8ea5..ee10c83 100644 --- a/modules/module1/InClass/finding_files.ipynb +++ b/modules/module1/InClass/finding_files.ipynb @@ -128,7 +128,7 @@ "outputs": [], "source": [ "%%bash\n", - "find /home/jovyan -name 'README'" + "find /home/uu00180764 -name 'README'" ] }, { @@ -172,7 +172,7 @@ "outputs": [], "source": [ "%%bash\n", - "find /home/jovyan/work/decart_bootcamp_part1 -name '*.ipynb'\n" + "find /home/uu00180764/work -name '*.ipynb'\n" ] }, { @@ -199,7 +199,8 @@ "metadata": {}, "outputs": [], "source": [ - "%%bash\n" + "%%bash\n", + "find /home/uu00180764/DATA -name '*.wav'\n" ] }, { @@ -208,7 +209,7 @@ "metadata": {}, "outputs": [], "source": [ - "mitral_files()" + "mitral_files(2)" ] }, { @@ -217,7 +218,7 @@ "metadata": {}, "outputs": [], "source": [ - "wave_files()" + "wave_files(11)" ] }, { @@ -258,7 +259,8 @@ "metadata": {}, "outputs": [], "source": [ - "%%bash" + "%%bash\n", + "find /home/uu00180764/DATA -name '*.txt' -size 10k | wc -1\n" ] }, { @@ -267,7 +269,7 @@ "metadata": {}, "outputs": [], "source": [ - "find_10k_files()" + "find_10k_files(71)" ] }, { @@ -293,7 +295,7 @@ "outputs": [], "source": [ "%%bash\n", - "find /home/jovyan \\( -name '*.db' -o -name '*.sqlite' \\)" + "find /home/uu00180764 \\( -name '*.db' -o -name '*.sqlite' \\)" ] }, { @@ -317,7 +319,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep chapel /home/jovyan/DATA/Misc/obits.txt" + "grep chapel /home/uu00180764/DATA/Misc/obits.txt" ] }, { @@ -334,7 +336,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep -i chapel /home/jovyan/DATA/Misc/obits.txt" + "grep -i chapel /home/uu00180764/DATA/Misc/obits.txt" ] }, { @@ -351,7 +353,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep -i -c chapel /home/jovyan/DATA/Misc/obits.txt" + "grep -i -c chapel /home/uu00180764/DATA/Misc/obits.txt" ] }, { @@ -368,7 +370,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep -i -c -r chapel /home/jovyan/DATA/Misc" + "grep -i -c -r chapel /home/uu00180764/DATA/Misc" ] }, { @@ -385,7 +387,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep -i -l -r chapel /home/jovyan/DATA/Misc" + "grep -i -l -r chapel /home/uu00180764/DATA/Misc" ] }, { @@ -402,8 +404,8 @@ "outputs": [], "source": [ "%%bash\n", - "grep -i chapel /home/jovyan/DATA/Misc/obits.txt \\\n", - "/home/jovyan/DATA/Misc/icd9-short.txt" + "grep -i chapel /home/uu00180764/DATA/Misc/obits.txt \\\n", + "/home/uu00180764/DATA/Misc/icd9-short.txt" ] }, { @@ -413,7 +415,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep -i chapel /home/jovyan/DATA/Misc/*.txt" + "grep -i chapel /home/uu00180764/DATA/Numerics/mimic2/hr/subjects/*.txt" ] }, { @@ -434,7 +436,10 @@ "outputs": [], "source": [ "%%bash\n", - "grep '7.-year-old' /home/jovyan/DATA/Misc/*.txt" + "grep -i '2..' /home/uu00180764/DATA/Numerics/mimic2/hr/subjects/*.txt > /home/uu00180764/work/hr_200.txt\n", + "cat /home/uu00180764/work/hr_200.txt\n", + "grep -i '2..' /home/uu00180764/DATA/Numerics/mimic2/bp/subjects/*.txt > /home/uu00180764/work/bp_200.txt\n", + "cat /home/uu00180764/work/bp_200.txt" ] }, { @@ -485,7 +490,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.5" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module1/InClass/introducing_shells.ipynb b/modules/module1/InClass/introducing_shells.ipynb index 13f3fa7..f2f0d09 100644 --- a/modules/module1/InClass/introducing_shells.ipynb +++ b/modules/module1/InClass/introducing_shells.ipynb @@ -86,7 +86,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.2" + "version": "3.7.3" }, "latex_envs": { "LaTeX_envs_menu_present": true, diff --git a/modules/module1/InClass/navigating_file_system.ipynb b/modules/module1/InClass/navigating_file_system.ipynb index a15b9db..6d36c40 100644 --- a/modules/module1/InClass/navigating_file_system.ipynb +++ b/modules/module1/InClass/navigating_file_system.ipynb @@ -287,9 +287,9 @@ "metadata": {}, "outputs": [], "source": [ - "number_of_files = -1\n", - "largest_file = \"None\"\n", - "most_recent_file = \"None\"" + "number_of_files = 8\n", + "largest_file = \"Accidents7904.csv\"\n", + "most_recent_file = \"seinfeldFood.sqlite\"" ] }, { @@ -340,7 +340,7 @@ "source": [ "%%bash\n", "cd\n", - "mkdir Test1/test1_a" + "mkdir -p Test1/test1_a" ] }, { @@ -469,7 +469,13 @@ "outputs": [], "source": [ "%%bash\n", - "ls -ltr /home/jovyan/DATA/Misc" + "ls -ltr /home/uu00180764/DATA/Misc\n", + "\n", + "mkdir -p OutbreakDetection/ChiefComplaints\n", + "cd OutbreakDetection\n", + "mkdir Obituaries\n", + "mkdir Sales\n", + "mkdir -p SocialMedia/Twitter\n" ] }, { @@ -649,7 +655,7 @@ "metadata": {}, "outputs": [], "source": [ - "navigating_quizzes.file_creator_quiz()" + "navigating_quizzes.file_creator_quiz()\n" ] }, { @@ -762,7 +768,8 @@ "outputs": [], "source": [ "%%bash\n", - "# Write the correct command below\n" + "# Write the correct command below\n", + "mv /home/uu00180764/DATA/Misc/obits.txt ~/work/OutbreakDetection/Obituaries/obits.txt\n" ] }, { @@ -894,7 +901,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.2" + "version": "3.7.3" }, "latex_envs": { "LaTeX_envs_menu_present": true, diff --git a/modules/module1/InClass/pipes.ipynb b/modules/module1/InClass/pipes.ipynb index 0e31858..c739f94 100644 --- a/modules/module1/InClass/pipes.ipynb +++ b/modules/module1/InClass/pipes.ipynb @@ -59,7 +59,7 @@ "outputs": [], "source": [ "%%bash\n", - "ls -l /home/jovyan/DATA/Misc | grep icd" + "ls -l /home/uu00180764/DATA/Misc | grep icd" ] }, { @@ -77,7 +77,8 @@ "metadata": {}, "outputs": [], "source": [ - "%%bash\n" + "%%bash\n", + "grep 'Oct. 17' /home/uu00180764/DATA/Misc/obits.txt | wc -l" ] }, { @@ -86,7 +87,7 @@ "metadata": {}, "outputs": [], "source": [ - "oct_17()" + "oct_17(6)" ] }, { @@ -128,7 +129,8 @@ "metadata": {}, "outputs": [], "source": [ - "%%bash\n" + "%%bash\n", + "grep -c -i '[Term]' /home/uu00180764/DATA/Misc/doid.obo " ] }, { @@ -137,7 +139,7 @@ "metadata": {}, "outputs": [], "source": [ - "concepts()" + "concepts(89527)" ] }, { @@ -189,7 +191,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module1/InClass/working_in_jupyter.ipynb b/modules/module1/InClass/working_in_jupyter.ipynb index f02a0f5..10a0285 100644 --- a/modules/module1/InClass/working_in_jupyter.ipynb +++ b/modules/module1/InClass/working_in_jupyter.ipynb @@ -20,6 +20,60 @@ "A Markdown cell, a Python code cell, and an output cell are shown below." ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Welcome to a [Jupyter](https://jupyter.org/) Notebook\n", + "\n", + "Jupyter notebooks are an open-source standard for creating what the authors describe as [literate computing](http://blog.fperez.org/2013/04/literate-computing-and-computational.html), a concept derived from Donald Knuth's [literate programming](https://en.wikipedia.org/wiki/Literate_programming).\n", + "\n", + "There is a vigorous debate about what is [good](https://blog.jupyter.org/jupyter-receives-the-acm-software-system-award-d433b0dfe3a2) and [bad](https://conferences.oreilly.com/jupyter/jup-ny/public/schedule/detail/68282) about notebooks. Most of the negative critiques stem from issues of software engineering, but as a means of *communicating* compuation, Jupyter notebooks have become very prevalent and liked.\n", + "\n", + "From the perspective of this class, Jupyter notebooks provide a (relatively) easy way for us to explore computation: all you need is a web browser (and a [GitHub](https://github.com/) account).\n", + "\n", + "Notebooks are made up of **cells** and there are three (kind of) types of cells.\n", + "1. Markdown cells. This is a markdown cell. Markdown cells are great for using language and media to instruct and explain. Markdown is a kind of markup language that allows us to format text (e.g. bold, emphasis, hyperlinks, lists, etc.)\n", + "2. Code cells. Code cells allow us to write and execute code. For the DeCART classes this will be code written in Python (the language from which Juptyer grew), but Juptyer supports many programming languages. You can see a list of supported languages [here](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels).\n", + "3. Output cells. Program cells produce output, which for the sake of simplicity I'm going to describe as being a cell.\n", + "\n", + "A Markdown cell, a Python code cell, and an output cell are shown below." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Welcome to a [Jupyter](https://jupyter.org/) Notebook\n", + "\n", + "Jupyter notebooks are an open-source standard for creating what the authors describe as [literate computing](http://blog.fperez.org/2013/04/literate-computing-and-computational.html), a concept derived from Donald Knuth's [literate programming](https://en.wikipedia.org/wiki/Literate_programming).\n", + "\n", + "There is a vigorous debate about what is [good](https://blog.jupyter.org/jupyter-receives-the-acm-software-system-award-d433b0dfe3a2) and [bad](https://conferences.oreilly.com/jupyter/jup-ny/public/schedule/detail/68282) about notebooks. Most of the negative critiques stem from issues of software engineering, but as a means of *communicating* compuation, Jupyter notebooks have become very prevalent and liked.\n", + "\n", + "From the perspective of this class, Jupyter notebooks provide a (relatively) easy way for us to explore computation: all you need is a web browser (and a [GitHub](https://github.com/) account).\n", + "\n", + "Notebooks are made up of **cells** and there are three (kind of) types of cells.\n", + "1. Markdown cells. This is a markdown cell. Markdown cells are great for using language and media to instruct and explain. Markdown is a kind of markup language that allows us to format text (e.g. bold, emphasis, hyperlinks, lists, etc.)\n", + "2. Code cells. Code cells allow us to write and execute code. For the DeCART classes this will be code written in Python (the language from which Juptyer grew), but Juptyer supports many programming languages. You can see a list of supported languages [here](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels).\n", + "3. Output cells. Program cells produce output, which for the sake of simplicity I'm going to describe as being a cell.\n", + "\n", + "A Markdown cell, a Python code cell, and an output cell are shown below." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, { "cell_type": "markdown", "metadata": {}, @@ -47,7 +101,13 @@ "```JSON\n", "{\n", " \"cell_type\": \"code\",\n", - " \"execution_count\": 1,\n", + " \"execution_count\": 1," + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ " \"metadata\": {},\n", " \"outputs\": [\n", " {\n", @@ -88,6 +148,20 @@ "1. Can you find any interesting ways to change or customize the behavior of the notebooks?" ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "Number 3 1. Click on up/down arrows\n", + "2. Edit-->Move cell up/down\n", + "3. Command mode: move cell up/down\n", + "4. Edit-->Copy/paste\n", + "5. Click on two papers button ('copy'). Click on clipboard icon ('paste').\n", + "6. Command mode: copy/paste" + ] + }, { "cell_type": "code", "execution_count": null, @@ -116,7 +190,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.2" + "version": "3.7.3" }, "latex_envs": { "LaTeX_envs_menu_present": true, diff --git a/modules/module1/ROADMAP.ipynb b/modules/module1/ROADMAP.ipynb index 7bf36ae..f261d70 100644 --- a/modules/module1/ROADMAP.ipynb +++ b/modules/module1/ROADMAP.ipynb @@ -71,7 +71,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.2" + "version": "3.7.3" }, "latex_envs": { "LaTeX_envs_menu_present": true, diff --git a/modules/module2/InClass/compression.ipynb b/modules/module2/InClass/compression.ipynb index 936ae2d..9ccf2fd 100644 --- a/modules/module2/InClass/compression.ipynb +++ b/modules/module2/InClass/compression.ipynb @@ -106,7 +106,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module2/InClass/remote_data.ipynb b/modules/module2/InClass/remote_data.ipynb index 2f03225..ce55201 100644 --- a/modules/module2/InClass/remote_data.ipynb +++ b/modules/module2/InClass/remote_data.ipynb @@ -243,6 +243,15 @@ "![]()" ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "![unknown](~/work/images_curl/04.jpg)\n" + ] + }, { "cell_type": "code", "execution_count": null, @@ -267,7 +276,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module2/InClass/ssh_scp.ipynb b/modules/module2/InClass/ssh_scp.ipynb index 8c4846e..c9c982f 100644 --- a/modules/module2/InClass/ssh_scp.ipynb +++ b/modules/module2/InClass/ssh_scp.ipynb @@ -202,13 +202,17 @@ ] }, { - "cell_type": "code", - "execution_count": null, + "cell_type": "markdown", "metadata": {}, - "outputs": [], "source": [ - "%%bash \n", - "pip install markdown" + "Kewei Xu\n", + "PhD student\n", + "School of Biological Science\n", + "\n", + "Phone Number: 201-233-7391\n", + "Email: kewei.xu@utah.edu\n", + "\n", + "![Utah Logo](https://healthcare.utah.edu/rebrand/img/logos/uhealth-logo.svg)" ] }, { @@ -227,7 +231,7 @@ "metadata": {}, "outputs": [], "source": [ - "display_bc(\"business_card_friend.md\")" + "display_bc(\"business_card_kewei.md\")" ] }, { @@ -323,7 +327,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module2/InClass/vi.ipynb b/modules/module2/InClass/vi.ipynb index b60bee7..cba57bd 100644 --- a/modules/module2/InClass/vi.ipynb +++ b/modules/module2/InClass/vi.ipynb @@ -187,6 +187,20 @@ "In the same directory as this notebook there are two text files: ``discharge_summary.txt`` and ``radiology.txt``. These are reports taken from the MIMIC2 data set that have been de-identified to remote names, dates, and locations to meet HIPAA safe harbor criteria. Use ``vim`` to \"de-de-identify\" the reports; that is, replace the substituted terms with realistic actual values." ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, { "cell_type": "markdown", "metadata": {}, @@ -218,7 +232,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module2/InClass/viewing_files.ipynb b/modules/module2/InClass/viewing_files.ipynb index 3b28c4c..3944f4f 100644 --- a/modules/module2/InClass/viewing_files.ipynb +++ b/modules/module2/InClass/viewing_files.ipynb @@ -55,7 +55,7 @@ "outputs": [], "source": [ "%%bash\n", - "cat /home/jovyan/DATA/Misc/obits.txt" + "cat /home/uu00180764/DATA/Misc/obits.txt" ] }, { @@ -72,7 +72,7 @@ "outputs": [], "source": [ "%%bash\n", - "cat /home/jovyan/DATA/Misc/obits.txt /home/jovyan/DATA/README.txt" + "cat /home/uu0180764/DATA/Misc/obits.txt /home/uu00180764/DATA/README.txt" ] }, { @@ -115,7 +115,7 @@ "outputs": [], "source": [ "from viewing_quizzes import *\n", - "oct15(ocount=-1)" + "oct15(ocount=6)" ] }, { @@ -142,7 +142,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module3/InClass/Index.ipynb b/modules/module3/InClass/Index.ipynb index 018d2ea..ba1b732 100644 --- a/modules/module3/InClass/Index.ipynb +++ b/modules/module3/InClass/Index.ipynb @@ -69,7 +69,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module3/InClass/compression.ipynb b/modules/module3/InClass/compression.ipynb index 187f7f1..63bb52d 100644 --- a/modules/module3/InClass/compression.ipynb +++ b/modules/module3/InClass/compression.ipynb @@ -93,7 +93,7 @@ "outputs": [], "source": [ "import compression_quizzes as cq\n", - "cq.examine_img(\"/home/jovyan/DATA/Images/PE/Ser_000006/IM-0124-0097.dcm\")" + "cq.examine_img(\"/home/uu00180764/DATA/Images/PE/Ser_000006/IM-0124-0097.dcm\")" ] }, { @@ -135,7 +135,7 @@ "outputs": [], "source": [ "import PIL\n", - "fname = \"/home/jovyan/work/nci/04\"\n", + "fname = \"/home/uu00180764/work/images_wget/04\"\n", "for q in range(100, 0, -10):\n", " PIL.Image.open(fname+\".jpg\").save(\"%s_%03d.jpg\"%(fname,q), quality=q)\n", "# Save a TIFF for reference\n", @@ -156,7 +156,7 @@ "outputs": [], "source": [ "%%bash\n", - "ls -lS /home/jovyan/work/nci" + "ls -lS /home/uu00180764/work/images_wget" ] }, { @@ -166,7 +166,7 @@ "outputs": [], "source": [ "from IPython.display import Image\n", - "Image(\"/home/jovyan/work/nci/04_070.jpg\")" + "Image(\"/home/uu00180764/work/images_wget/04_010.jpg\")" ] }, { @@ -275,13 +275,13 @@ "gzip -c ~/DATA/Misc/carotid.txt > ~/work/compression/carotid.txt.gz\n", "gzip -l ~/work/compression/carotid.txt.gz\n", "\n", - "gzip -c /home/jovyan/DATA/Images/PE/Ser_000006/IM-0124-0097.dcm > ~/work/compression/IM-0124-0097.dcm\n", + "gzip -c /home/uu00180764/DATA/Images/PE/Ser_000006/IM-0124-0097.dcm > ~/work/compression/IM-0124-0097.dcm\n", "gzip -l ~/work/compression/IM-0124-0097.dcm\n", "\n", - "gzip -c ~/work/nci/04.jpg > ~/work/compression/04.jpg.gz\n", + "gzip -c ~/work/images_wget/04.jpg > ~/work/compression/04.jpg.gz\n", "gzip -l ~/work/compression/04.jpg.gz\n", "\n", - "gzip -c ~/work/nci/04_.tiff > ~/work/compression/04_.tiff.gz\n", + "gzip -c ~/work/images_wget/04_.tiff > ~/work/compression/04_.tiff.gz\n", "gzip -l ~/work/compression/04_.tiff.gz" ] }, @@ -380,7 +380,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4,