Merge pull request #70 from imr-framework/mri4all_console

Mri4all console

README.md

@@ -8,7 +8,7 @@
 
 Virtual Scanner is an end-to-end hybrid Magnetic Resonance Imaging (MRI) simulator/console designed to be zero-footprint, modular, and supported by open-source standards.
 
-This project is a winning response to the [ISMRM 2019 Junior Fellow Challenge (Africa)](https://www.ismrm.org/2019-junior-fellow-challenge/africa/), which poses the task of boosting accessibility to MRI training resources for underserved areas such as sub-Saharan Africa. We designed Virtual Scanner to help develop local expertise in these areas so that sustained deployment of MRI hardware is possible. Importantly, Virtual Scanner will be continually developed as a research tool that provides functionalities for simulating and prototyping MRI acquisition methods as well as services for sharing computational methods and resources with researchers around the world. Please read our publication in the journal of open source software [here](https://joss.theoj.org/papers/10.21105/joss.01637).
+This project is a winning response to the [ISMRM 2019 Junior Fellow Challenge (Africa)](https://www.ismrm.org/2019-junior-fellow-challenge/africa/), which poses the task of boosting accessibility to MRI training resources for underserved areas such as sub-Saharan Africa. We designed Virtual Scanner to help develop local expertise in these areas so that sustained deployment of MRI hardware is possible. Importantly, Virtual Scanner will be continually developed as a research tool that provides functionalities for simulating and prototyping MRI acquisition methods as well as services for sharing computational methods and resources with researchers around the world. Please read our publication in the journal of open souce software [here](https://joss.theoj.org/papers/10.21105/joss.01637).
 
 Virtual Scanner consists of two modes: in Standard Mode, a console-like GUI allows users to perform virtual scans and conduct basic analysis; in Advanced Mode, modular simulation/analysis of the entire signal chain may be performed.  
 
@@ -71,35 +71,15 @@ Read the API documentation [here](https://imr-framework.github.io/virtual-scanne
 ## Standard Mode
 * The **Register** page allows you to choose a phantom for simulation. Its format is similar to the form for entering information of the subject when conducting real scans. Choose the "Numerical" phantom for all simulations now.
 
-<p align="center"> <a>
-<img title="Register Screenshot" src="https://github.com/imr-framework/virtual-scanner/blob/master/virtualscanner/coms/coms_ui/static/screenshots/register.JPG" width="600">
-</a></p>
-
 * The **Acquire** page allows the user to choose either a Gradient Echo (GRE) or a Spin Echo (SE, with optional inversion recovery) sequence, enter the parameters, and simulate them on a cylindrical phantom ("Numerical") containing spheres with different T1, T2, and PD values.
 
-<p align="center"> <a>
-<img title="Register Screenshot" src="https://github.com/imr-framework/virtual-scanner/blob/master/virtualscanner/coms/coms_ui/static/screenshots/acquire.JPG" width="600">
-</a></p>
-
 * The **Analyze** page allows the user to load a series of data acquired in ISMRM/NIST phantom for T1 or T2 mapping and conduct curve fitting to obtain T1 and T2 maps. In addition, it can detect spheres in the phantom, a feature useful for comparing generated parameter values to literature values.
 
-<p align="center"> <a>
-<img title="Register Screenshot" src="https://github.com/imr-framework/virtual-scanner/blob/master/virtualscanner/coms/coms_ui/static/screenshots/analyze.JPG" width="600">
-</a></p>
-
 ## Advanced Mode
 * The **Tx** (RF transmit) page allows one to calculate and plot SAR from pulseq .seq files. *This feature is under development.*
 
-<p align="center"> <a>
-<img title="Register Screenshot" src="https://github.com/imr-framework/virtual-scanner/blob/master/virtualscanner/coms/coms_ui/static/screenshots/tx.JPG" width="600">
-</a></p>
-
 * The **Rx** (RF receive) page allows one to visualize time-domain MR signal, generated from an arbitrary grayscale image, and see the effects of using different demodulation frequencies and ADC sampling rate. *This feature is under development.*
 
-<p align="center"> <a>
-<img title="Register Screenshot" src="https://github.com/imr-framework/virtual-scanner/blob/master/virtualscanner/coms/coms_ui/static/screenshots/rx.png" width="600">
-</a></p>
-
 * Other features, including phantom and sequence viewers and reconstruction methods, are in active development.
 
 ## Known Issues

_build/_images/favicon_io (17)/site.webmanifest

@@ -0,0 +1 @@
+{"name":"","short_name":"","icons":[{"src":"/android-chrome-192x192.png","sizes":"192x192","type":"image/png"},{"src":"/android-chrome-512x512.png","sizes":"512x512","type":"image/png"}],"theme_color":"#ffffff","background_color":"#ffffff","display":"standalone"}

_images/favicon_io (17)/site.webmanifest

@@ -0,0 +1 @@
+{"name":"","short_name":"","icons":[{"src":"/android-chrome-192x192.png","sizes":"192x192","type":"image/png"},{"src":"/android-chrome-512x512.png","sizes":"512x512","type":"image/png"}],"theme_color":"#ffffff","background_color":"#ffffff","display":"standalone"}

console/__init__.py

@@ -0,0 +1 @@
+name = "virtual-scanner"

console/coms/coms_ui/GUI_test_functions.py

@@ -0,0 +1,272 @@
+from selenium import webdriver
+from selenium.common.exceptions import TimeoutException
+from selenium.webdriver.support.ui import WebDriverWait # available since 2.4.0
+from selenium.webdriver.support import expected_conditions as EC # available since 2.26.0
+from selenium.webdriver.common.by import By
+import time
+import subprocess
+import sys
+import unittest
+from selenium.webdriver.common.action_chains import ActionChains
+import webbrowser
+
+from virtualscanner.utils.constants import COMS_UI_PATH
+
+#subprocess.call(['python', str(constants.COMS_UI_PATH / 'coms_server_flask.py')], shell=True)
+
+# Create a new instance of the Firefox driver
+
+
+class GUItestclass(unittest.TestCase):
+    def get_vs_address(self):
+        print(sys.platform)
+        if sys.platform == 'win32':
+            vs_address = "http://127.0.0.1:5000/"
+        else:
+            vs_address = "http://0.0.0.0:5000/"
+
+        return vs_address
+
+    def setup_driver(self):
+        if sys.platform == 'win32':
+            driver_path = str(COMS_UI_PATH / "firefox_driver/geckodriver_windows.exe")
+        else:
+            driver_path = str(COMS_UI_PATH / "firefox_driver/geckodriver_mac")
+        print("Firefox driver path: ", driver_path)
+        driver = webdriver.Firefox(executable_path=driver_path)
+        # Go to Virtual Scanner
+
+        return driver
+
+    def run_test(self, test, expected_value):
+        driver = self.setUp()
+        value = test(driver)
+        print("Expected value: ", expected_value)
+        print("Test value: ", value)
+        assert value == expected_value, "Value is not the same as expected :("
+        driver.quit()
+
+        return value==expected_value
+
+
+    def login_std(self, driver):
+        # What does an implicit wait do?
+        driver.find_element_by_id("mode-selection").submit()
+        time.sleep(3)
+        result = driver.current_url
+        return result
+
+
+    def login_adv(self, driver):
+        driver.find_element_by_id("opt2").click()
+        time.sleep(1)
+        driver.find_element_by_id("mode-selection").submit()
+        time.sleep(3)
+        result = driver.current_url
+        return result
+
+
+    def register(self, driver):
+        # Login first
+        self.login_std(driver)
+
+        # Find register button and click
+        driver.find_element_by_id("reg-form-submit").click()
+        time.sleep(3)
+
+        # Check and return style of element with id="success-sentence"
+        success_sentence = driver.find_element_by_id("success-sentence")
+        time.sleep(3)
+        result = success_sentence.get_attribute("style") == "display: block;"
+       # return success_sentence.get_attribute("style")
+        return result
+
+
+    def acquire(self, driver):
+        self.register(driver)
+
+        driver.find_element_by_link_text("Acquire").click()
+        time.sleep(2)
+
+        orientations = ['axial']
+        seq_types = ['GRE']
+
+        result = None
+
+        for orientation in orientations:
+            for seq_type in seq_types:
+                ir = False
+                if seq_type == 'IRSE':
+                    seq_name = 'SE'
+                    ir = True
+                else:
+                    seq_name = seq_type
+
+                # Add sequence
+                driver.find_element_by_id("addseq-btn").click() #
+                time.sleep(1)
+                driver.find_element_by_link_text(seq_name).click()
+                time.sleep(1)
+
+                # Change parameters for faster sim (5 x 5)
+                inputnx = driver.find_element_by_id("Nx")
+                inputnx.clear()
+                inputnx.send_keys("5")
+                driver.find_element_by_id("Ny").click()
+
+                # Inversion recovery
+                if ir:
+                    driver.find_element_by_id("IRSE-check").click()
+
+                # Simulate
+                driver.find_element_by_css_selector(".submit-form-btn").click()
+
+                element_found_result = False
+                # Wait until image is shown
+                try:
+                    element = WebDriverWait(driver, 300).until(
+                         EC.presence_of_element_located((By.XPATH,"/html/body/div/div/div/div/div/div/img[1]"))
+                    )
+                    element_found_result = element is not None
+
+                finally:
+                    result = element_found_result
+
+                # If image is not shown after a while, raise error
+                # Print success text
+        return result
+
+    def analyze(self, driver):
+        self.register(driver)
+        driver.find_element_by_link_text("Analyze").click()
+        time.sleep(2)
+
+        # T1 mapping
+        driver.find_element(By.ID, "load-btn").click()
+        element = driver.find_element(By.ID, "ui-id-4")
+        actions = ActionChains(driver)
+        actions.move_to_element(element).perform()
+        time.sleep(1)
+        t1 = driver.find_element(By.ID, "ui-id-6")
+        actions.move_to_element(t1).click().perform()
+
+        time.sleep(0.5)
+        driver.find_element(By.CSS_SELECTOR, ".btn:nth-child(1)").click()
+
+        t2_result = False
+        try:
+            element = WebDriverWait(driver, 600).until(
+                EC.presence_of_element_located((By.XPATH, "/html/body/div/div/div/img[1]"))
+            )
+            t2_result = element is not None
+
+        finally:
+            result = t2_result
+
+        time.sleep(3)
+        return result
+
+
+    def tx(self, driver):
+        self.login_adv(driver)
+        driver.find_element_by_xpath("/html/body/div/div/nav/ul/li/a[@href=\"/tx\"]").click()
+        time.sleep(1)
+        result = driver.current_url
+        return result
+        # How do you load a file?
+        #C:\Users\tongg\Documents\Research\Code\virtual-scanner\virtualscanner\server\rf\tx\SAR_calc\assets
+
+    def rx(self, driver):
+        self.login_adv(driver)
+
+        driver.find_element_by_xpath("/html/body/div/div/nav/ul/li/a[@href=\"/rx\"]").click()
+        time.sleep(1)
+        input_dsf = driver.find_element_by_id("dsf")
+        input_dsf.clear()
+        input_dsf.send_keys("2")
+
+        time.sleep(1)
+
+        driver.find_element_by_id("form-submit-btn").click()
+        result = False
+        try:
+            element = WebDriverWait(driver, 20).until(
+                #                    EC.presence_of_element_located((By.ID, "num0"))
+                EC.presence_of_element_located((By.XPATH, "/html/body/div/div/div/div[contains(text(),'Resulting Image')]"))
+
+            )
+            result = element is not None
+
+        finally:
+            return result
+
+    def test_login_std(self):
+        driver1 = self.setup_driver()
+        driver1.get(self.get_vs_address())
+        self.assertEqual(self.login_std(driver1), self.get_vs_address()+"register")
+        driver1.quit()
+
+    def test_login_adv(self):
+        driver2 = self.setup_driver()
+        driver2.get(self.get_vs_address())
+        self.assertEqual(self.login_adv(driver2),self.get_vs_address()+"recon")
+        driver2.quit()
+
+    def test_register(self):
+        driver3 = self.setup_driver()
+        driver3.get(self.get_vs_address())
+        self.assertTrue(self.register(driver3))
+        driver3.quit()
+
+    def test_acquire(self):
+        driver4 = self.setup_driver()
+        driver4.get(self.get_vs_address())
+        self.assertTrue(self.acquire(driver4))
+        driver4.quit()
+
+
+    def test_analyze(self):
+        driver5 = self.setup_driver()
+        driver5.get(self.get_vs_address())
+        self.assertTrue(self.analyze(driver5))
+        driver5.quit()
+
+    def test_tx(self):
+        driver6 = self.setup_driver()
+        driver6.get(self.get_vs_address())
+        self.assertEqual(self.tx(driver6),self.get_vs_address()+"tx")
+        driver6.quit()
+
+    def test_rx(self):
+        driver7 = self.setup_driver()
+        driver7.get(self.get_vs_address())
+        self.assertTrue(self.rx(driver7))
+        driver7.quit()
+
+
+
+    # def launch_tests():
+    #     vsadr = get_vs_address()
+    #     tx_address = vsadr + "tx"
+    #    # webbrowser.open(vsadr)
+    #     print(vsadr)
+    #     # Run tests
+    #     run_test(login_adv, vsadr + "recon")
+    #     run_test(login_std, vsadr + "register")
+    #     run_test(tx, tx_address)
+    #
+    #     run_test(register, "display: block;")
+    #     run_test(acquire, "success")
+    #     #    run_test(analyze, "success") # This takes a long time (T2 mapping)
+    #     run_test(rx, "success")
+    #     #webbrowser.close()
+    #
+    #     return "Test Code"
+
+
+
+
+if __name__ == '__main__':
+    unittest.main()
+
+