diff --git a/02_activities/assignments/assignment_2.ipynb b/02_activities/assignments/assignment_2.ipynb index 36a3e2bb7..70dfb0203 100644 --- a/02_activities/assignments/assignment_2.ipynb +++ b/02_activities/assignments/assignment_2.ipynb @@ -63,7 +63,7 @@ "id": "JhJAJb1m-nkn" }, "source": [ - "## 1. Reading and Displaying Data from the First File\n", + "## 1. Read and Displaying Data from the First File\n", "\n", "With the list of the relevant `inflammation_xx.csv` file paths above, write a program to read the `inflammation_xx.csv` files, and display the contents of the first file in this list.\n", "\n", @@ -76,8 +76,145 @@ "metadata": { "id": "n0m48JsS-nMC" }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "0,0,1,3,1,2,4,7,8,3,3,3,10,5,7,4,7,7,12,18,6,13,11,11,7,7,4,6,8,8,4,4,5,7,3,4,2,3,0,0\n", + "\n", + "0,1,2,1,2,1,3,2,2,6,10,11,5,9,4,4,7,16,8,6,18,4,12,5,12,7,11,5,11,3,3,5,4,4,5,5,1,1,0,1\n", + "\n", + "0,1,1,3,3,2,6,2,5,9,5,7,4,5,4,15,5,11,9,10,19,14,12,17,7,12,11,7,4,2,10,5,4,2,2,3,2,2,1,1\n", + "\n", + "0,0,2,0,4,2,2,1,6,7,10,7,9,13,8,8,15,10,10,7,17,4,4,7,6,15,6,4,9,11,3,5,6,3,3,4,2,3,2,1\n", + "\n", + "0,1,1,3,3,1,3,5,2,4,4,7,6,5,3,10,8,10,6,17,9,14,9,7,13,9,12,6,7,7,9,6,3,2,2,4,2,0,1,1\n", + "\n", + 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"0,1,2,2,2,3,6,6,6,7,6,3,11,12,13,15,15,10,14,11,11,8,6,12,10,5,12,7,7,11,5,8,5,2,5,5,2,0,2,1\n", + "\n", + "0,0,2,1,3,5,6,7,5,8,9,3,12,10,12,4,12,9,13,10,10,6,10,11,4,15,13,7,3,4,2,9,7,2,4,2,1,2,1,1\n", + "\n", + "0,0,1,2,4,1,5,5,2,3,4,8,8,12,5,15,9,17,7,19,14,18,12,17,14,4,13,13,8,11,5,6,6,2,3,5,2,1,1,1\n", + "\n", + "0,0,0,3,1,3,6,4,3,4,8,3,4,8,3,11,5,7,10,5,15,9,16,17,16,3,8,9,8,3,3,9,5,1,6,5,4,2,2,0\n", + "\n", + "0,1,2,2,2,5,5,1,4,6,3,6,5,9,6,7,4,7,16,7,16,13,9,16,12,6,7,9,10,3,6,4,5,4,6,3,4,3,2,1\n", + "\n", + "0,1,1,2,3,1,5,1,2,2,5,7,6,6,5,10,6,7,17,13,15,16,17,14,4,4,10,10,10,11,9,9,5,4,4,2,1,0,1,0\n", + "\n", + "0,1,0,3,2,4,1,1,5,9,10,7,12,10,9,15,12,13,13,6,19,9,10,6,13,5,13,6,7,2,5,5,2,1,1,1,1,3,0,1\n", + "\n", + "0,1,1,3,1,1,5,5,3,7,2,2,3,12,4,6,8,15,16,16,15,4,14,5,13,10,7,10,6,3,2,3,6,3,3,5,4,3,2,1\n", + "\n", + "0,0,0,2,2,1,3,4,5,5,6,5,5,12,13,5,7,5,11,15,18,7,9,10,14,12,11,9,10,3,2,9,6,2,2,5,3,0,0,1\n", + "\n", + "0,0,1,3,3,1,2,1,8,9,2,8,10,3,8,6,10,13,11,17,19,6,4,11,6,12,7,5,5,4,4,8,2,6,6,4,2,2,0,0\n", + "\n", + "0,1,1,3,4,5,2,1,3,7,9,6,10,5,8,15,11,12,15,6,12,16,6,4,14,3,12,9,6,11,5,8,5,5,6,1,2,1,2,0\n", + "\n", + "0,0,1,3,1,4,3,6,7,8,5,7,11,3,6,11,6,10,6,19,18,14,6,10,7,9,8,5,8,3,10,2,5,1,5,4,2,1,0,1\n", + "\n", + "0,1,1,3,3,4,4,6,3,4,9,9,7,6,8,15,12,15,6,11,6,18,5,14,15,12,9,8,3,6,10,6,8,7,2,5,4,3,1,1\n", + "\n", + "0,1,2,2,4,3,1,4,8,9,5,10,10,3,4,6,7,11,16,6,14,9,11,10,10,7,10,8,8,4,5,8,4,4,5,2,4,1,1,0\n", + "\n", + "0,0,2,3,4,5,4,6,2,9,7,4,9,10,8,11,16,12,15,17,19,10,18,13,15,11,8,4,7,11,6,7,6,5,1,3,1,0,0,0\n", + "\n", + "0,1,1,3,1,4,6,2,8,2,10,3,11,9,13,15,5,15,6,10,10,5,14,15,12,7,4,5,11,4,6,9,5,6,1,1,2,1,2,1\n", + "\n", + "0,0,1,3,2,5,1,2,7,6,6,3,12,9,4,14,4,6,12,9,12,7,11,7,16,8,13,6,7,6,10,7,6,3,1,5,4,3,0,0\n", + "\n", + "0,0,1,2,3,4,5,7,5,4,10,5,12,12,5,4,7,9,18,16,16,10,15,15,10,4,3,7,5,9,4,6,2,4,1,4,2,2,2,1\n", + "\n", + "0,1,2,1,1,3,5,3,6,3,10,10,11,10,13,10,13,6,6,14,5,4,5,5,9,4,12,7,7,4,7,9,3,3,6,3,4,1,2,0\n", + "\n", + "0,1,2,2,3,5,2,4,5,6,8,3,5,4,3,15,15,12,16,7,20,15,12,8,9,6,12,5,8,3,8,5,4,1,3,2,1,3,1,0\n", + "\n", + "0,0,0,2,4,4,5,3,3,3,10,4,4,4,14,11,15,13,10,14,11,17,9,11,11,7,10,12,10,10,10,8,7,5,2,2,4,1,2,1\n", + "\n", + "0,0,2,1,1,4,4,7,2,9,4,10,12,7,6,6,11,12,9,15,15,6,6,13,5,12,9,6,4,7,7,6,5,4,1,4,2,2,2,1\n", + "\n", + "0,1,2,1,1,4,5,4,4,5,9,7,10,3,13,13,8,9,17,16,16,15,12,13,5,12,10,9,11,9,4,5,5,2,2,5,1,0,0,1\n", + "\n", + "0,0,1,3,2,3,6,4,5,7,2,4,11,11,3,8,8,16,5,13,16,5,8,8,6,9,10,10,9,3,3,5,3,5,4,5,3,3,0,1\n", + "\n", + "0,1,1,2,2,5,1,7,4,2,5,5,4,6,6,4,16,11,14,16,14,14,8,17,4,14,13,7,6,3,7,7,5,6,3,4,2,2,1,1\n", + "\n", + "0,1,1,1,4,1,6,4,6,3,6,5,6,4,14,13,13,9,12,19,9,10,15,10,9,10,10,7,5,6,8,6,6,4,3,5,2,1,1,1\n", + "\n", + "0,0,0,1,4,5,6,3,8,7,9,10,8,6,5,12,15,5,10,5,8,13,18,17,14,9,13,4,10,11,10,8,8,6,5,5,2,0,2,0\n", + "\n", + "0,0,1,0,3,2,5,4,8,2,9,3,3,10,12,9,14,11,13,8,6,18,11,9,13,11,8,5,5,2,8,5,3,5,4,1,3,1,1,0\n", + "\n" + ] + } + ], "source": [ + "'''Python program to evaluate the effectiveness of a medication got reducing arthritis inflammation flare-ups. \n", + "Data from 60 patients, across 40 days for 12 session files is available.\n", + "User can select and display session data, one file at a time (Part 1).\n", + "Summary statistics (mean, max, and min) are calulated by patient record (Part 2).\n", + "Program returns an bool value of True if an irregularity exists in the pateient data (Part 3).\n", + "Data irregularity is defined as a session file with one or more patient data with a mean inflammation of zero.\n", + "'''\n", + "\n", + "# Part 1: Display data from selected file in named file path\n", + "\n", "all_paths = [\n", " \"../../05_src/data/assignment_2_data/inflammation_01.csv\",\n", " \"../../05_src/data/assignment_2_data/inflammation_02.csv\",\n", @@ -94,9 +231,13 @@ "]\n", "\n", "with open(all_paths[0], 'r') as f:\n", - " # YOUR CODE HERE: Use the readline() or readlines() method to read the .csv file into a variable\n", - " \n", - " # YOUR CODE HERE: Iterate through the variable using a for loop and print each row for inspection" + " # Read the .csv file into the variable file_contents\n", + " file_contents = f.readlines()\n", + "\n", + " # Iterate through the variable file_contents using a for loop and print each row for inspection\n", + " # Use \"for row in\"command to print list items in rows for inspection ease\n", + " for row in file_contents:\n", + " print(row)\n" ] }, { @@ -136,27 +277,36 @@ }, "outputs": [], "source": [ + "# Part 2: Use Python numpy library to calculate three summary statistics on a speccified patient (n) by day (p) session (file) within a function named patient_summary\n", + "\n", + "# Import Numerical Python into this program application under the np alias\n", "import numpy as np\n", "\n", + "# Create a function named patient_summary to compute summary statistics for each patient's data over a 40-day period for the file session specified in Part 1\n", "def patient_summary(file_path, operation):\n", " data = np.loadtxt(fname=file_path, delimiter=',') # Load the data from the file\n", " ax = 1 # This specifies that the operation should be done for each row (patient)\n", "\n", " # Implement the specific operation based on the 'operation' argument\n", + " # Use the mean, max, and min numpy summary operations for each patient over 40 days\n", " if operation == 'mean':\n", - " # YOUR CODE HERE: Calculate the mean (average) number of flare-ups for each patient\n", + " # Calculate the mean (average) number of flare-ups for each patient\n", + " summary_values = np.mean(data, axis=1)\n", "\n", " elif operation == 'max':\n", - " # YOUR CODE HERE: Calculate the maximum number of flare-ups experienced by each patient\n", + " # Calculate the maximum number of flare-ups experienced by each patient\n", + " summary_values = np.max(data, axis=1)\n", "\n", " elif operation == 'min':\n", - " # YOUR CODE HERE: Calculate the minimum number of flare-ups experienced by each patient\n", + " # Calculate the minimum number of flare-ups experienced by each patient\n", + " summary_values = np.min(data, axis=1)\n", "\n", " else:\n", " # If the operation is not one of the expected values, raise an error\n", " raise ValueError(\"Invalid operation. Please choose 'mean', 'max', or 'min'.\")\n", "\n", - " return summary_values" + " return summary_values\n", + " " ] }, { @@ -165,9 +315,17 @@ "metadata": { "id": "3TYo0-1SDLrd" }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "60\n" + ] + } + ], "source": [ - "# Test it out on the data file we read in and make sure the size is what we expect i.e., 60\n", + "# Test data file output to ensure the size is what we expect (i.e., 60)\n", "# Your output for the first file should be 60\n", "data_min = patient_summary(all_paths[0], 'min')\n", "print(len(data_min))" @@ -234,7 +392,7 @@ }, "outputs": [], "source": [ - "# Run this cell so you can use this helper function\n", + "# Run this cell to use it as helper function in Part 3\n", "\n", "def check_zeros(x):\n", " '''\n", @@ -257,23 +415,39 @@ }, "outputs": [], "source": [ - "# Define your function `detect_problems` here\n", + "# Part 3: Evaluate if the session file contains one or more patient mean inflammation scores of zero.\n", "\n", "def detect_problems(file_path):\n", - " #YOUR CODE HERE: Use patient_summary() to get the means and check_zeros() to check for zeros in the means\n", - "\n", - " return" + " # Use the patient_summary() fucntion to get the session patient mean scores and use the check_zeros() to evaluate whether at least one or more patient man scores > 0\n", + " # Read patient data from the session file, specified in the Part 1 file_path\n", + " # Assign the patient_summary mean operation value to mean_result\n", + " mean_result = patient_summary(file_path, operation = 'mean')\n", + "\n", + " # Use check-zeros output to decide if the mean_result function evaluates as True (at least one patient mean inflammation score in the array is equal to zero)\n", + " return check_zeros(mean_result)\n", + " " ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "False" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ - "# Test out your code here\n", - "# Your output for the first file should be False\n", - "print(detect_problems(all_paths[0]))" + "# The detect_problems function returns a check_zeros bool value = True if an irregularity exists in the pateient data;\n", + "# Otherwise, check_zeros bool value = False\n", + "detect_problems(all_paths[0])" ] }, { @@ -314,7 +488,8 @@ "provenance": [] }, "kernelspec": { - "display_name": "Python 3", + "display_name": "python-env", + "language": "python", "name": "python3" }, "language_info": { @@ -327,7 +502,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.8" + "version": "3.11.13" } }, "nbformat": 4,